thalljiscience/thalljiscience.github.io

{\rtf1\ansi\ansicpg1252\deff0\nouicompat\deflang1033\deflangfe1033{\fonttbl{\f0\fmodern\fprq1\fcharset0 Courier New;}{\f1\fswiss\fprq2\fcharset0 Calibri;}} {\colortbl ;\red0\green0\blue255;} {*\generator Riched20 10.0.19041}\viewkind4\uc1 \pard\nowidctlpar\f0\fs18 Readme File for BioEdit v7.7.1.0\par \par BioEdit is a graphical biological sequence editor that runs on\par Windows 95, 98, NT, 2000, XP, 7, 8 and 10. The purpose of this program is \par to provide a useful molecular biology tool which can be started \par up and used easily with as little effort required as possible to \par learn the program.\par \par * DISCLAIMER **\par \par The author makes no guarantee as to the fitness or \par suitability of this software for any purpose. BioEdit\par is offered as is and no responsibility will befall the \par author for any problems caused by or correlated with the \par use of this software, including, but not limited to, \par damages, non-suitability, misuse, data loss, or wasted time. \par \par * By choosing to install this software you are accepting \par the terms of this license. If you do not want to accept these\par terms, you must not install the software *****\par ---------------------------------------------------------------------\par \par Contents of this File:\par -- Files shipped with the BioEdit v7.7.1.0 installation\par -- Features included in BioEdit v7.7.1.0\par -- Accessory applications included with installation.\par -- Installing TreeView\par -- Installing ReadSeq for 64-bit machines\par -- Bug fixes/changes since last version\par -- How to contact the author\par \par ---------------------------------------------------------------------\par \par Files shipped with the BioEdit v7.7.1.0 installation:\par \par The following files and folders are installed to the directory\par in which you install BioEdit:\par \par In installation directory:\par \par The installation folder will also contain the following files:\par \tab _deisreg.isr\par \tab _isreg32.dll\par \tab BioEdit.exe (main program)\par \tab DeIsL1.isu\par \tab ReadSeqv202.zip (64-bit implementation of ReadSeq sequence format converter)\par \tab TreeV32.zip (the TreeView installation distribution)\par \tab TreeView.txt (TreeView information)\par \tab HttpClient.dll (required for NCBI connectivity)\par \tab msvcr120d.dll (required for NCBI connectivity)\par \tab license.txt (license agreement)\par \tab Readme.txt (this file)\par \par apps (accessory applications, Web pages and WWW bookmarks)\par \tab accApp.ini\par \tab blast.txt\par \tab btblastall.exe\par \tab blastcl3.exe\par \tab blastcli.exe\par \tab bookmark.txt\par \tab cap.doc\par \tab cap.EXE\par \tab clustalw.exe\par \tab clustalw.txt\par \tab DNADIST.DOC\par \tab dnadist.exe\par \tab DNAML.DOC\par \tab dnaml.exe\par \tab DNAMLK.DOC\par \tab DNAMLK.EXE\par \tab DNAPARS.DOC\par \tab DNAPARS.EXE\par \tab DOS4GW.EXE\par \tab fastDNAml.doc\par \tab fastdnaml.EXE\par \tab FITCH.DOC\par \tab Fitch.exe\par \tab btformatdb.exe\par \tab KITSCH.DOC\par \tab KITSCH.EXE\par \tab NEIGHBOR.DOC\par \tab NEIGHBOR.EXE\par \tab ncbi_presets.ini\par \tab phylip.map\par \tab PROML.DOC\par \tab\lang1036 proml.exe\par \tab promlk.exe\par \tab PROTDIST.DOC\par \tab PROTDIST.EXE\par \tab PROTPARS.DOC\par \tab PROTPARS.EXE\par \tab\lang1033 readseq.exe\par \tab ReadSeq.txt\par \par \par database (empty folder)\par \tab\par \par help\par \tab BioEdit.cnt\par \tab BioEdit.GID (not installed -- will appear after the first time help is accessed)\par \tab Bioedit.hlp\par \par sounds\par \tab A small list of small sound files containing individual character reads\par \par tables\par \tab Bacterial_phylogeny.tab\par \tab BLOSUM62\par \tab BLOSUMcoloring.tab\par \tab chao_fasman.tab\par \tab codon.tab\par \tab codonDegeneracyColoring.tab\par \tab color.tab\par \tab dayhoff\par \tab defcolor.tab\par \tab enzyme.tab\par \tab GC.VAL\par \tab gencodes.tab\par \tab gonnet\par \tab IDENTIFY\par \tab kyteDoolittle.tab\par \tab KyteDoolittleHydrophobicityColoring.tab\par \tab ManuelRuizColorTable.tab\par \tab match\par \tab PAM120\par \tab\lang1046 Pam250\par \tab PAM250Coloring.tab\par \tab PAM40\par \tab PAM80\par \tab SEQCODE.VAL\par \tab taxGroups.tab\par \tab Viral_Phylogeny.tab\par \tab\par \par ---------------------------------------------------------------------\par \tab\tab\tab\par \lang1033 Features included in BioEdit v7.7.1.0:\par \par -- An easy, graphical interface for sequence manipulation \par and editing, modeled after SeqApp and SeqPup (Don Gilbert).\par -- Variable editing options, including 'select and drag' sliding and \par 'grab and drag' sliding of residues, variable selection options, \par mouse-click insert and delete of gaps, full column selecting, \par on-screen editing with cut, copy and paste, and auto-scrolling of \par edit window.\par -- Anchor columns to protect aligned areas.\par -- Read and edit ABI and SCF sequence files, display traces with several \par options (reverse complement, select, copy, export, scale, zoom).\par -- Print ABI files with professional-looking formatted output and file\par header information.\par -- Batch conversion of ABI to SCF format sequence traces. \par -- Group sequences into groups or families.\par -- Lock alignment of grouped sequences for synchronized hand alignment \par adjustements.\par -- Annotate sequences with graphical features with dynamic view in\par alignment windows including feature anntation information tooltips. \par -- Lock sequences to prevent accidental edits.\par -- Specify characters to be considered valid for calculations in amino acid \par and nucleotide sequences.\par -- Sort sequences by name, LOCUS, DEFINITION, ACCESSION, PID/NID, REFERENCES,\par COMMENTS or by residue frequency in a selected column. \par -- Verbally read back sequences in single sequene editor to verify hand-typed\par sequence entries.\par -- Configure accessory application interfaces to run external analysis \par programs through a graphical interface created by BioEdit. \par Automatically feed information to and retrieve files from external apps. \par External apps run in a separate thread to allow simultaneous use of BioEdit \par while running time-consuming processes. Output from an external program \par may be automatically opened by another program.\par -- Split window for simultaneous editing of two different places in the same \par file.\par -- Merge alignments through a reference sequence.\par -- Append one alignment to the end of another.\par -- View phylip trees, manipulate nodes, and print trees.\par -- Configure your own menu shortcuts for alignment windows.\par -- Block copying of residues to clipboard allowing for pasting of full \par alignments or parts of alignments into a word processor.\par -- Basic sequence manipulations (copy/paste of sequences between documents, \par translation and degenerate encoding, RNA->DNA->RNA, reverse/complement, \par upper/lowercase).\par -- Multiple document interface (Maximum of 20 open alignment documents at a \par time, but no set limit on other open windows).\par -- Plasmid Drawing and graphical annotation\par -- Dynamic memory allocation with support for up to 20,000 sequences per \par document. Sequences up to 4.6 million bases (the E. coli genome) and \par alignments >6000 seqs (the prokaryotic 16S rRNA alignment) have been tested.\par -- Open and save large alignment files quickly with the BioEdit Project binary\par file format.\par -- Formatted translations of nucleic acid sequences with codon usage summary, \par choice of one- or three-letter amino acid codes, translation of selected\par region only of nucleic acid, and choice of start/stop codons \par -- Six-Frame translation of nucleic acid sequences into Fasta-format ORF lists. \par Tested by successfully translating entire E. coli genome (4.6 Mbases) into \par 10,125 sorted raw codon stretches of 100 or more amino acids and 39,880 \par unsorted raw codon stretches of 50 or more amino acids. \par -- Amino acid and nucleotide composition analyses and plots\par -- Align protein-encoding nucleic acid sequences through amino acid translation.\par -- ClustalW multiple sequence alignment (interface internal, external program by \par Des Higgins et. al.) with auto-update of aligned protein full titles and \par GenBank field information, as well as nucleotide coding sequence when aligned \par from a protein view of nucleotide sequences. \par -- Protein hydrophobicity/hydrophilicity plots\par -- Protein hydrophobic moment matrices calculated from 0-180 degrees\par -- Full choice of system fonts now available in edit window\par -- 'Revert to Saved' and 'undo' functions. \par -- Edit both amino acid and nucleic acid sequences.\par -- Easy point-and-click color table editing, with different tables for protein \par and nucleic acid sequences.\par -- Alignment-responsive shading based on information content of alignment positions.\par -- Identity / Similarity shading in alignment window with user-defined threshold.\par -- BioEdit currently reads and writes BioEdit, GenBank, Fasta, NBRF/PIR, \par Phylip 3.2 and Phylip 4 formats.\par -- Additionally reads (but does not write) Clustal and GCG formats\par -- Autodetect of sequence format -- just double click the file and go!\par -- Open and import sequences and alignments in any compatible format right\par from the clipboard\par -- Import/Export filter for 10 additional formats (Using Don Gilbert's ReadSeq).\par ReadSeq auto-detects the sequence format as well -- 64-bit port by Mathew D. Pagel\par -- Import/Append one file on to the end of another (regardless of file format).\par Import also auto-detects format\par -- Basic rich-text editor.\par -- Restriction mapping with any or all-frames translation, multiple enzyme and \par output options and circular DNA option. Manually choose custom lists of enzymes\par for restriction maps\par -- Choose restriction enzymes by manufacturer\par -- Auto-linking to your favorite Web Browser (e.g., Netscape or Internet Explorer).\par -- World Wide Web Bookmarks \par -- NCBI BLAST tools, including BLAST 2.0 Internet client and local BLAST with \par the ability to compile local databases from Fasta files\par -- Configurable formatted text print with dynamic print preview,\par -- Configurable formatted shaded graphical output with dynamic preview, identity \par and similarity shading, and ability to cut and paste directly to \par graphics/presentation program for generation of figures.\par -- Rich text export of formatted, shaded alignment.\par -- RNA secondary structure comparative analysis tools, including covariation, \par potential pairings, and mutual information analyses.\par -- 2-D matrix plotter for mutual information output with dynamic data viewing \par with the mouse pointer. (Also allows image copy/paste and bitmap save).\par -- View sections of very large matrices with plotter (tested on up to 5183x5183 \par matrix = 180 Mb file)\par -- Paste over sequence blocks and sequence titles\\par -- Search and replace in titles with wildcards\par -- Store taxonomy inforation for sequences and map taxonomies directly from master \par taxonomy tables\par -- Retrieve sequences and sequence-associated pubmed references directly from the WWW.\par \par ---------------------------------------------------------------------\par \par Accessory applications included with this installation \par (preconfigured for use with BioEdit):\par \par \tab\par \tab blastall -- Authors: Stephen Altschul, Warren Gish, Webb Miller, \par Eugene W. Myers and David J. Lipman \par \tab blasctcl3 -- Authors: Stephen Altschul, Warren Gish, Webb Miller, \par Eugene W. Myers and David J. Lipman \par \tab CAP -- Author: Xiaoqiu Huang\par \tab ClustalW -- Authors: Des Higgins, Toby Gibson, Julie Thompson.\par \tab\tab\tab\tab Rebuilt by Tom Hall (main code not modified) to run \par \tab\tab\tab\tab under Windows XP)\par \tab DNAdist -- Author: Joe Felsenstein\par \tab DNAml -- Author: Joe Felsenstein \par \tab DNAmlk -- Author: Joe Felsenstein\par \tab DNAPars -- Author: Joe Felsenstein\par \tab FastDNAml -- Authors: Gary J. Olsen, Hideo Matsuda, Ray Hagstrom, \par and Ross Overbeek \par \tab Fitch -- Author: Joe Felsenstein \par \tab formatdb -- Authors: Stephen Altschul, Warren Gish, Webb Miller, \par Eugene W. Myers and David J. Lipman \par \tab Kitsch -- Author: Joe Felsenstein \par \tab Neighbor -- Author: Joe Felsenstein\par \tab Proml -- Author: Joe Felsenstein \par \tab Protdist -- Author: Joe Felsenstein \par \tab Protpars -- Author: Joe Felsenstein \par \tab readSeq -- Author: Don Gilbert, 64-bit port by Mathew D. Pagel\par \tab TreeView -- Author: Roderic D.M. Page\par \par If distribution of any of these programs becomes a problem, any or all may have \par to be removed in future releases. However, the BioEdit configuration interface \par makes it relatively easy to add applications to the BioEdit Accessory Applications \par menu.\tab \par \par ---------------------------------------------------------------------\par Installing TreeView:\par \par TreeView is a phylogenetic tree viewing program written by Roderic \par D.M. Page. Previous versions of BioEdit included a distribution of\par the TreeView executable and supporting libraries in the apps folder. \par At the request of the author full TreeView installation is now \par distributed with BioEdit. This installation is contained within the \par file called TreeView.zip.\par \par To install TreeView, unzip the file to a temporary directory, then run\par the program called "setup.exe" which will be created. TreeView will \par install itself on your system.\par \par To configure TreeView to run through the accessory apps menu of BioEdit, \par choose Add/Remove/Modify an Accessory Application from the Accessory \par Application menu. In the "Name of Accessory" box, type \ldblquote TreeView\rdblquote . \par Press "Specify" next to the \ldblquote Program\rdblquote Box and browse to the new location \par for the TreeView.exe program. Check the box called \ldblquote Prompt for input\par file\rdblquote . In the \ldblquote General Description\rdblquote box, type \ldblquote TreeView version 1.5.2. \par Copyright Roderic D.M. Page, 1998. r.page@bio.gla.ac.uk. \par

\pard {{\field{*\fldinst{HYPERLINK http://www.taxonomy.zoology.gla.ac.uk/rod/rod.html }}{\fldrslt{http://www.taxonomy.zoology.gla.ac.uk/rod/rod.html\ul0\cf0}}}}\f0\fs18\rdblquote without any carriage \par returns. Then press \ldblquote Add / Modify\rdblquote at the bottom of the dialog. Upon \par closing the window, you will be prompted to have BioEdit close and restart. \par For more information on installing accessory applications, see Configuring \par and Using External Applications in the BioEdit on-line help.\par

\pard\brdrb\brdrs\brdrw15\brsp20 \nowidctlpar\par

\pard\nowidctlpar\par Note For Windows 7, 64-bit users of TreeView:\par The version of TreeView distributed with BioEdit will not work correctly. \par Rod Page offers an updated version of TreeView at\par

\pard {{\field{*\fldinst{HYPERLINK http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download.html }}{\fldrslt{http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download.html\ul0\cf0}}}}\f0\fs18\par that does work well on this platform. To install this version such that \par it works with pre-configured Phylip accessory apps within BioEdit, it is \par best to override the default installation directory when installing \par TreeViewX to C:\Program Files\Rod Page\TreeView. You can then either \par 1.) Change the name of the file C:\Program Files\Rod Page\TreeView\tv.exe to \par C:\Program Files\Rod Page\TreeView\treev32.exe or 2.) modify accessory \par application configurations to point to C:\Program Files\Rod Page\TreeView\tv.exe.\par \par ---------------------------------------------------------------------\par \par Installing ReadSeq for 64-bit machines:\par Don Gilbert's original readSeq sequence converter was a 16-bit application and\par does not operate on 64-bit Windows machines, even in compatibility mode. \par Mathew D. Pagel has produced a Java-based port readSeq that worked flawlessly when\par I tested it. The original distribution of version 2.02 from \par {{\field{*\fldinst{HYPERLINK https://code.google.com/p/readseq/downloads/detail?name=ReadSeqv202.zip&can=2&q= }}{\fldrslt{https://code.google.com/p/readseq/downloads/detail?name=ReadSeqv202.zip&can=2&q=\ul0\cf0}}}}\f0\fs18\par is included in the BioEdit installation with the author's permission to allow users\par to install a compatible version of readSeq if they wish. Follow the instructions in\par the file "Instructions.txt" found in ReadSeqv202.zip within your BioEdit installation\par directory after installing BioEdit to install the updated port of readSeq.\par \par ---------------------------------------------------------------------\par \par BioEdit has not been regularly maintained for several years, however, a few \par updates have been made simply to keep the program generally functional.\par The following list is not complete because the time has not been available to \par adequately keep track. The help file has not been updated to reflect most changes:\par \par Since v7.2.6:\par -- Rebuilt program to restore Ctrl+Right click functionality for reference sequence choice.\par \par Since v7.2.4:\par -- Added functionality for https to fix download of sequence data from NCBI.\par \par Since v7.1.11:\par -- The dot-plot feature for pairwise sequence comparison was brought back by request from \par a user (Under Sequence->Pairwise alignment->Dot Plot (pairwise comparison).\par -- Taxonomy mapping from sequence title was brought back under Sequence->Phylogeny / \par Taxonomy->Extract Taxonomy->(three mapping options). Only bacterial and viral\par taxonomies are supported by default, but a custom table can be made by opening the file \par

\\tables\\\f1\fs22 \f0\fs18 Bacterial_phylogeny.tab or \\tables\\\f1\fs22 \f0\fs18 Viral_Phylogeny.tab, \par copying the contents into MS Excel, and creating a custom table according to the same\par general template, then saving the custom file as a tab-delimited file. If time permits,\par an auto-map of taxonomy from NCBI may be added in the future for convenience.\par -- A preferences option to not write to C:\\Windows\\ncbi.ini when performing BLAST-related\par functions was added to work around the error received by users without read/write access\par to the C:\\Windows directory. This may mean one needs to manually create ncbi.ini within\par C:\\Windows as a one-time event (or have the IT department do it for those without access\par privileges on the computer.\par \par Since v7.0.9:\par -- The pairwise alignment function was fixed to agree with examples in the help \par documentation.\par -- Right-click context menu added to title panel in sequence document.\par -- Support for local BLAST and accessory application launching fixed in \par Windows 7 64-bit version.\par -- GenBank sequence retrieval updated.\par -- String-to-floating point number conversion problems (hopefully) fixed for \par European computers with particular regional settings.\par -- Single-sequence translation in selected frames with codon usage reporting \par was fixed. There was a memory bug when translated sequence was not an exact \par multiple of three in length.\par -- Associating a phylogenetic tree with an alignment from the phylogenetic tree view \par was fixed.\par -- Six-frame translations were fixed to allow producing ORF lists from multiple \par sequences at once.\par -- Added option to save six-frame translations to a file rather than loading \par directly into text editor.\par \pard\brdrb\brdrs\brdrw15\brsp20 \nowidctlpar\par \pard\nowidctlpar\par The following changes and/or fixes have been made since version v7.0.8:\par -- The restriction map utility was fixed. It was broken by the relocation \par of the BioEdit.ini file to the program install directory.\par -- An option was put into the preferences to allow temporary redirecting \par of file paths for blast database creation and search execution to the \par root directory. The reason for this is that if the name of the database \par directory (when doing a search) or source directory for a fasta file \par (when converting to a blast database) is too long, it can overload the \par maximum command line length for running blastall.exe or formatdb.exe\par (the NCBI command-line programs used for blast utilities).\par \par \par The following changes and/or fixes have been made since version v7.0.7:\par -- Moved BioEdit.ini to the program current run directory. Hopefully this will \par help on computers without write access to the system folder.\par \par The following changes and/or fixes have been made since version v7.0.5:\par -- Updated NCBI sequence retrieval to deal with recent changes at NCBI that broke the sequence retrieval functions in the \par previous version.\par -- Note: (not a change, per se): Scoring in pairwise alignment functions does not agree with the example in the help \par document. This will be investigated if/when I have time. I had considered removing the functions, but decided no to on \par the grounds that they generally work OK for quick manipulations and can be useful as a time-saving utility. They should \par not, however, be used as a teaching tool.\par \par The following changes and/or fixes have been made since version v7.0.4:\par -- Changing proxy setting for sequence retrieval from GenBank had no \par affect because the routine was looking in the wrong directory for the\par BioEdit.ini file.\par \par The following changes and/or fixes have been made since version v7.0.3:\par -- A bug in sequence retrieval from GenBank fixed that caused retrievals \par to come back saying " ... format unrecognized".\par \par The following changes and/or fixes have been made since version v7.0.2:\par -- A memory bug in RNA covariation routine was fixed.\par \par The following changes and/or fixes have been made since version v7.0.1:\par -- The blast programs blastall and formatdb were modified to allow passing\par parameters in a file as well as on the command line to get around the \par Windows xommand line length limit\par -- blastall and formatdb were modified to allow passing a darabase name\par with spaces (original verion tries to parse the name into multiple\par file names)\par -- When launching an alignment file from the Windows Explorer, BioEdit now\par tries to open the file in an existing BioEdit instance if there is one\par open, rather than opening a new one.\par -- Updated installer will hopefully take care of the trouble some people \par have been having installing BioEdit \par \par The following changes and/or fixes have been made since version v7.0.0:\par -- The optimal pairwise alignment routine was inadvertently overwritten \par with a test version that was only functional on nucleic acid sequences. \par This caused pairwise alignment on amino acid sequences to fail. \par The original alignment method was put back.\par \par The following changes and/or fixes have been made since version v6.0.7:\par -- Documentation (online help file) was updated for the first time \par since version 5.0.6.\par -- Automatic links to NCBI BLAST via the World Wide Web were added back \par with current NCBI pages with editable addresses.\par -- Error on doing local blast searches when swap directory contained \par spaces fixed. However, BLAST won't work if entire command line is \par too long for Windows, so keeping the BioEdit swap directory in a \par path name as short as possible (e.g. C:\\BioEdit\\Temp) is a good idea.\par -- Some context-sensitive help added (not complete).\par -- Fixed bug in graphic view that caused Error when view is plotted in\par dot conservation mode and the "reference" sequence is shorter than\par one of the alignment sequences.\par -- Fixed a bug in floating point conversion with non-English regional\par settings (when a ',' is used as decimal separator) that would cause\par an error when trying to translate nucleotide sequences into protein \par (bug manifested when reading in the "codon.tab" file and converting\par frequency numbers -- the regional settings were not being detected\par properly).\par -- Added support for mouse wheel in Alignment document window. Clicking\par the mouse wheel button toggles between vertical and horizontal scroll\par function.\par -- Fixed bug in right-click-based gap deletion in grouped sequences with\par group-locked alignment status (gaps were being deleted only for edited\par sequence and no entire locked group).\par -- A couple of other bugs relating to adding or deleting gaps around a \par residue with the right mouse button in a sequence which is a member \par of an alignment-locked grouped were fixed. Behavior was updated to \par only operate upon sequences that are not grouped together in an \par alignment-locked group with the sequence in question.\par -- Fixed bug in clustal auto-link that caused VERSION field to be lost\par in aligned sequences.\par -- Removed the sort function "selected sequences by residue frequencies"\par This was a one-time utility that does not work as the title implies and\par was not supposed to be present in the public version.\par -- Removed "Group top-down by identical sequences" under Sort menu. This\par function did not make much sense for most contexts.\par \par The following changes and/or fixes have been made since version v6.0.6:\par This is a list of counterintuitive changes to deal with a set of \par counterintuitive features in the short term\par \par -- Removed automatic taxonomy mapping support -- its undocumented and caused \par confusion.\par -- Removed primer pair/oligo mapping and Tm calculation -- undocumented and \par caused confusion.\par -- Removed query functions for sequence features -- again, undocumented and \par caused confusion.\par \par The following changes and/or fixes have been made since version v6.0.5:\par \par -- Removed "Auto-update View Options" because it causes long delays in \par Win2000 and XP.\par -- Fixed a bug in Graphic View new to v6.0.5 causing access violation \par if View Features mode is on in document window.\par \par The following changes and/or fixes have been made since version v5.0.9:\par Note that this list is not complete: \par -- Some memory troubles with grouped sequences fixed. Using sequence \par groups is now more stable.\par -- Access violations when deleting sequences in dot conservation mode \par or vertically scrolling very long alignments in dot conservation mode \par fixed.\par -- Retrieve sequences directly from GenBank over the WWW.\par -- Automatically retrieve GenBank info from GenBank for existing\par sequences for Genbank-fasta formatted titles\par (eg. gi|16082679|ref|NC_003132.1|).\par -- Automatically retrieve Pubmed references for GenBank sequences.\par -- Restriction on number of sequences removed. All memory allocation\par for sequences was made dynamic.\par -- Paste over sequence blocks to quickly create subalignments based upon\par a region of a larger alignment or produce alignment concatenations. \par -- Paste over titles, and paste onto (concatenate to) titles.\par -- Copy sequence titles added in a couple of variations.\par -- Copy nucleic acid sequence blocks in reverse complemented orientation\par -- Copy sequences in a tab-delimited format (for pasting into a \par spreadsheet)\par -- Find/replace function for sequence information\par -- flexible find/replace in titles with indexed wildcards\par -- filter leading and trailing characters off of sequence titles.\par -- Find titles equal to, beginning with, or containing lists of strings.\par -- Unique based upon sequences or title with a two-step sort + select \par & delete process to remove redundant sequences or titles\par -- Query sequences by data by TITLE, LOCUS, DEFINITION, ACCESSION, \par VERSION / GI, PID (or SID), DBSOURCE, KEYWORDS, REFERENCES, FEATURES, \par COMMENT, and/or Phylogeny.\par -- Invert selection of sequences or residues\par -- Edit information for multiple sequences at once with Sequence-->Edit\par all selected.\par -- Extract subsequences (including orientation for DNA) from lists of\par coordinates (with choice of alignment-gapped or true positions) \par -- Query and extract annotated sequence features.\par -- Map true positions from lists of alignment positions.\par -- Add tabulated taxonomy information to sequences.\par -- Several variable ways of renaming titles in batch mode \par (Sequence-->Rename-->...)\par -- Several ways to filter out sequences based upon inclusion/exclusion\par of specific characters, length, or number of leading, trailing, or \par total gaps.\par -- Sort by phylogeny\par -- Invert current sequence order\par -- Map oligos and primer pairs to alignments based upon mismatch threshold\par -- Calculate DNA oligo Tm's with mismatches based upon thermodynamic\par parameters from John SantaLucia's lab.\par -- Calculate Tm's for oligos and compare them to same region of other \par sequences from alignment window using right mouse button clicks.\par -- Several operations on local sequence region selection with right \par mouse button click.\par -- Speed enhanced on pairwise alignment of large similar sequences\par -- Align sequences to an existing alignemnt by pairwise alignment to\par phylogenetic near neighbor in existing alignment.\par -- Choose individual restriction enzymes when creating a restriction map.\par -- Easily flush an alignment out with gaps to produce a rectangular matrix\par \par The following changes and/or fixes have been made since version v5.0.8:\par -- Made a minor adjustment to preferences for characters to be treated\par as resides -- There's an option to either include them as positions\par or ignore them completely fro similarity/ID shading.\par -- Fixed a bug in pasting into the single sequence editor window.\par \par The following changes and/or fixes have been made since version v5.0.7:\par -- Protein alignments in new installations may have shading problems\par because when the option to explicitly specify all characters to be\par considered valid for calculations (including ID/similarity shading),\par 'N' was accidentally missed for amino acids. Several installations \par probably have gone out with 'N' missing from the list of amino acids.\par This can cause protein alignments to have similarity/identity shading\par errors. 'N' has been put back into the default.\par -- Access violations that could occurr when typing in an RNA structure \par mask while in RNA base pair coloring mode, and when there is a non-\par symmetric number of openeing vs. closing brackets. This has been \par fixed.\par \par The following changes and/or fixes have been made since version v5.0.6:\par -- Added base pair mask support for RNA alignments\par -- Added base-pair coloring for RNA alignments with user-defined color\par scheme\par -- Fixed bug in creating local Blast databases from within a sequence\par document\par \par The following changes and/or fixes have been made since version v5.0.5:\par -- Added support for phylogenetic trees without distance information.\par -- Added save function for phylogenetic trees.\par -- Added linking of phylogentic trees to an alignment.\par -- Multiple trees may be imported from one or several files.\par -- Incorporated phylogentic trees are saved with alignment in BioEdit\par alignment format.\par -- Added option to view trees with or without distance information.\par -- Updated sequence label editing to allow spaces in comments.\par \par The following changes and/or fixes have been made since version v5.0.4:\par -- Added node flipping to phylogenetic tree viewer.\par -- Added printing to phylogenetic tree viewer.\par -- Fixed bug in the "append alignments" (the first alignment was\par appended to itself) -- bugged version was only out for one day. \par \par The following changes and/or fixes have been made since version v5.0.3:\par -- Fixed some issues with accessory app linking (problems keep creeping\par up related to the change made in version 5.0.0 to specify a swap folder\par for temp files).\par -- Added the option to merge alignments by appending one alignment to the\par end of another.\par -- Added a ruimentary tree viewer (VERY unfinished -- only reads phylip\par trees, only in "phylogram" view, no distance ruler yet, no print, \par save or manipulate yet) -- The reason for having an internal tree\par viewer is to in the future allow flipping of nodes and resaving the \par tree for use in nicer tree viewing programs like TreeView that allow\par better formatting, but don't have manipulation options. Also, it \par would be nice in the future to directly link phylogenetic tree views\par to alignment files for quick phylogeny reference.\par \par The following changes and/or fixes have been made since version v5.0.2:\par -- Added column anchoring to protect areas that are already aligned.\par -- Updated translation toggling so that gaps that are expanded back\par from a single gap (when toggling from a protein view to a \par nucleotide view) are always "locked" (to avoid problems with \par inadvertently crunching off-screen gaps that spuriously toggled\par back as "unlocked" when aligning by hand).\par -- Fixed a bug that caused RNA covariation, potential pairings, or\par mutual information analyses to crash when "mask numbering" was\par chosen but there was no numbering mask specified.\par -- Fixed newly introduced bug the caused MI Examiner to crash when\par no masks are specified.\par \par The following changes and/or fixes have been made since version v5.0.1:\par -- Updated Mutual Information Examiner to handle lists of positions.\par -- Added several options to Mutual Information preferences to allow \par variable display of list information in MI Examiner.\par -- Added option to export and import color table files.\par -- Fixed a bug that caused color table to lock sometimes.\par -- Added option to toggle translations using the current selected residue\par as a reference frame.\par -- Fixed a bug that caused document to appear hung when sort by base\par frequency was chosen without a selected column.\par -- Added ability to sort by selected range of residues.\par -- No longer append sequence lengths to titles when saving Fasta files.\par -- Added preference (on "General" tab) to require verification for \par revert to saved function.\par -- Fixed problem with creating Local Blast databases which would occur \par on machines with no NCBI tools installed. \par -- Accessory apps and Blast Internet client are now launched through \par an auto-generated batch file.\par \par \par The following changes and/or fixes have been made since version v5.0.0:\par -- Added the option to specify user-defined temp (swap) directory for all\par temporary files and user-defined BLAST database directory so that \par BioEdit may be used from a drive space that does not allow writing \par (actually added to v5.0.0 a few days before 5.0.1 came out).\par -- Fixed some bugs associated with running accessory apps from version\par 5.0.0 after the temp directory option was added. \par \par The following changes and/or fixes have been made since version v4.8.10:\par (Probably missed a few -- I hadn't updated this file for a while)\par -- Added options to specify which characters in nucleic acid and amino \par acid sequences are considered to be valid for calculations.\par -- Added options for sorting sequences by title, LOCUS, DEFINITION, \par ACCESSION, PID/NID, REFERENCES, COMMENTS and residue frequency in\par a selected column.\par -- Added options to annotate sequences with graphical features, using the \par standard GenBank FEATURES tags as the standard for keeping track of \par annotation "type", but allowing full user control over feature names,\par descriptions, colors, shapes and positions.\par -- Added function to automatically annotate graphical features using \par existing GenBank FEATURES field\par -- Added options for grouping sequences into groups or families, with \par user-defined coloring of grouped titles and the option to lock the\par alignment of grouped sequences to allow synchronized hand alignment\par adjustments between grouped and locked sequences.\par -- Added option to lock individual sequences to prevent accidental edits.\par -- Updated the BioEdit file format to save graphical annotations, sequence\par group information, locked sequence information and positional flags.\par -- Added function to update previously saved BioEdit plasmid maps with a\par new restriction enzyme file when the ReBase file is changed (changing \par the enzyme.tab file can cause mis-indexing of restriction enzyme sites\par in existing plasmid files).\par -- Updated shaded graphic view to correctly do conservation (dot) view \par when that view mode is selected in the alignment window (no longer need\par to create a new dot-plotted alignment and any sequence can be used as the\par reference rather than just the top sequence).\par -- Added a "Overwrite" and "Insert" modes to both on-screen and single-\par sequence editor sequence editing.\par -- Updated local BLAST interface to feed multiple sequence automatically for \par a batch job, and to allow specification of a permanent file output and \par the option to open output automatically in the BioEdit text editor or not. \par -- Modified some menus (Edit and Sequence menus, mainly). The same options \par (and more) are still there, but submenus having been created to group \par certain related functions including: gap-realted functions, pairwise \par alignment functions, simple manipulations (reverse, uppercase, lowercase,\par remove numbers), and search functions.\par -- The "No BLAST" version (BioEdit without local BLAST packaged) was done\par away with -- it's too much of pain to duplicate everything but one extra\par function and make a whole independent installation when relatively few\par people download that one anyway).\par -- At the last minute -- added an option to verbally read back sequences \par (protein, nucleic acid, or anything else) to verify hand-typed sequence\par entries.\par -- The docuentation update is NOT yet completed, but is underway. Program\par documentation is still stuck at version 4.7.8.\par \par \par The following changes and/or fixes have been made since version v4.8.9:\par -- Fixed the (re-introduced) bug that caused floating point number\par formatting error when translating nucleic acid sequences on non-US\par regional settings machines\par -- Fixed a couple of bugs that affected reading in of sample name and \par version on ABI 310 files\par \par v4.8.8 -- forgot to document changes\par \par The following changes and/or fixes have been made since version v4.8.7:\par -- Removed the internal web browser\par -- Fixed a bug in codon frequency reporting (nucleotide translations)\par that caused floating point numbers to sometimes get jumbled up in \par the output\par -- Added a conservation plot toggle to the main alignment window with\par the option to choose the character to draw for a "conserved residue"\par (the "reference" sequence defaults to the first sequence in an \par alignment -- RIGHT-CLICK the mouse over any sequence to change it to\par the current reference sequence for this view option)\par -- Fixed a minor bug in setting of custom menu shortcuts for alignment\par documents. The "Import from clipboard" should now work with a \par user-defined menu shortcut.\par \par The following changes and/or fixes have been made since version v4.8.6:\par -- Added optimal pairwise alignment routine with a summary of percent\par identity and similarity (multiple choices for scoring matrix for \par amino acid alignment, user-defined gap initiate, gap extend and\par nucleotide match parameters, and option for global alignment or\par alignment allowing ends to slide over each other).\par -- Added routine to create an alignment that plots all residues that are\par identical to the top sequence in an alignment as a dot.\par -- Added a cheap version of a dot plotter for plotting matrix similarity\par between two sequences -- total sequence length product cannot exceed \par 2000 x 2000, however, so it's not useful for genome comparisons or \par or even moderately large sequences.\par -- Added option to calculate the similarity and/or identity between\par two sequences as they are aligned.\par \par The following changes and/or fixes have been made since version v4.8.5:\par -- 3/10/2000 -- added NCBI blastcl3 to distribution and added a more\par versatile linking interface for the BLAST client -- the old \par BLAST client 2 has apparently been disabled\par -- 3/10/2000 -- Added block convention to user-defined motif search. \par [] brackets indicate ambiguous residues and \{\} brackets indicate\par exclusions (eg [LIV] will accept 'L', 'I' or 'V', whereas \{LIV\} will\par accept anything BUT 'L', 'I' or 'V'.\par -- 3/10/2000 -- Fixed bug that caused an error and a blank doc to be \par opened when the alignment control bar was hidden\par -- 3/10/2000 -- Fixed a couple of bugs related to reading and writing\par of GenBank files (lines beginning with numbers were truncated and \par manually updating fields sometimes resulted in misformatting) \par -- Added an alignment merge funcion which merges two alignments based \par upon a standard common to both alignments\par -- Added batch export of ABI raw trace data.\par -- Fixed the recently introduced disabling of the ABI/SCF trace print\par option\par -- fixed metafile copy and print of reverse-complemented traces\par -- improved default scaling of SCF traces for printing and metafile copy\par -- fixed bug in graphic view which could affect first time use of \par the graphic view when used with non-US Windows regional settings \par \par The following changes and/or fixes have been made since version v4.8.4:\par \par -- 1/28/2000 -- Fixed bug that came out when creating a mask (must have \par been introduced in version 4.7.8). This bug caused two masks to be\par formed and sequence memory for the first two sequences to get \par cross-linked. (caused by accidentally re-assigning a memory pointer\par rather than an entire data structure).\par -- 1/25/2000 -- Fixed bug introduced with the last bug fix that causes \par name mangling of ClustalW 1.4 output and loss of GenBank info when\par running ClustalW 1.4 (the version distributed with BioEdit).\par -- Fixed potential bug that comes out if you replace the clustalw 1.4\par (the version distributed with BioEdit) with clustalw 1.8 in the \par apps folder -- clustalw 1.8 will rearrange the order of the input \par sequences, causing sequences and titles to become scrambled in the \par new alignment -- this has been fixed.\par -- Added raw data view and analyzed and raw data export from .abi trace \par files.\par -- Added option to change starting point of ruler bar in alignment window. \par \par The following changes and/or fixes have been made since version v4.8.3:\par \par -- 12/20/1999 -- Added helical wheel diagrams for proteins. Select a \par protein or portion of a protein and choose Sequence->Protein->Helical\par Wheel Diagram\par -- Fixed bug in accessory app launching that causes spaces to be lost in\par command prefixes for inputs and checkboxes\par -- Added option to accessory app launching to auto-feed sequences in \par separate files (eg, for Lalign from the Fasta package)\par \par The following changes and/or fixes have been made since version v4.8.2:\par \par -- 12/13/1999 -- Fixed bug in hydrophobic moment profiles -- had an \par exponent missing in Fourier equation \par -- 12/13/1999 -- Added hydrophobic moment matrix plots (0-180 degrees)\par -- 12/13/1999 -- fixed a couple of bugs in trace viewer that caused \par problems with non-U.S. regional settings\par -- 12/10/1999 -- Added support for SCF version 2.00 files\par \par The following changes and/or fixes have been made since version v4.8.1:\par \par -- 12/7/1999 -- Fixed problem of accessory application info getting \par overwritten when a full install is done with a new BioEdit version\par -- Added options to accessory application interface:\par 1. Bypass interface when running an accessory\par 2. Link output(s) of one accessory to another/other accessory(s)\par 3. Create accessory app links that are only called by other accessory\par links and do not show up on accessory app menu\par 4. Automatically truncate titles to 10 characters for programs\par that don't accept long names and/or change spaces to '_'\par 5. Rename redundant sequence names and generate a report file\par specifying title changes\par \par The following changes and/or fixes have been made since version v4.8.0:\par \par -- 12/2/1999 -- Fixed a bug in accessory application launching that could\par cause a memory error when running an app from a window that is not a \par sequence alignment document\par -- 12/1/1999 -- Fixed on-screen title editing so that double-clicking\par on a selected title still opens the sequence editing box and overrides\par title editing\par -- 12/1/1999 -- Added option to disable on-screen editing \par -- 12/1/1999 -- Fixed bug in consensus sequence generation. A consensus\par generated from less than all of the sequences in an alignment was using\par frequencies calculated using the total number of sequences rather than\par the selected number\par -- 12/1/1999 -- Fixed bug that caused an access violation when \par re-activating a document that had sequences deleted (introduced with\par version 4.7.8)\par -- A bug was fixed that caused a memory mix-up when pasting sequences in\par a document in a position other than the end\par \par The following changes and/or fixes have been made since version v4.7.9:\par \par -- Added support for SCF sequence trace files\par -- Added horizontal and vertical zoom controls to sequence trace form\par -- Added crosshairs with trace position reporting in trace form\par -- Added batch conversion of ABI files to SCF format\par -- Traces draw faster on the screen\par -- Fixed another bug in on-screen sequence title editing (when vertical\par bar was scrolled, it was causing trouble with the identity of the \par edited title)\par \par The following changes and/or fixes have been made since version v4.7.8:\par \par -- Fixed bug in local BLAST linking that caused failure when operating\par from a directory with a space in its name and using a mtrix other than\par Blosum62\par -- Fixed a similar bug in linking to ReadSeq for importing and exporting \par of extra file formats\par -- Added "Import from Clipboard" and "New from Clipboard" functions under\par the file menu -- Clipboard contents are treated exactly like a file and\par automatic linking to ReadSeq for importing formats that BioEdit does not\par internally read is maintained\par -- Added function for inserting multiple gaps at selected residue positions\par or at specified position in selected sequences\par -- Updated on-screen title editing -- use the arrow keys to scroll up and \par down when changing several titles in the same document\par -- Fixed a bug in plasmid drawing that caused a floating point error when \par adding a very short feature to a circular plasmid\par \par \par The following changes and/or fixes have been made since version v4.7.7:\par \par -- Bug that caused edits to sequence titles to also be inserted at cursor\par position when in Edit Residues mode was fixed on 11/17/99 (also caused\par a problem when using alt+ keystrokes to access menus in Edit mode)\par -- User-defined motif search function added for amino acid, nucleic acid,\par or simple text.\par -- Memory allocation for sequences changed to use less memory (memory was\par being allocated to set aside space for 20,000 sequence structures \par regardless of the number of sequences in a file -- now a single pointer \par is set aside for the max number of allowed sequences (20,000), but no\par memory is allocated until a sequence is created)\par -- Bug in ABI trace reader was fixed that caused trace / nucleotide colors\par to be mismatched when the file contained an order other than "GATC"\par -- The online help and printable documentation were updated on 11/8/1999\par \par \par The following changes and/or fixes have been made since version v4.7.6:\par \par -- ABI files may be edited and saved, and edited sequence may be reverted\par to the original, non-editable version. The edited sequence is opened\par as a sequence/alignment doc upon opening an ABI file.\par -- Extended capabilities of restriction mapping module. Long sequences\par may be mapped (tested up to 1.75 Mb on machine with 128 Mb RAM). My\par mapping procedure is pretty slow, but 500,000 bp runs in ~2 minutes \par on a 366 MHz Celeron). Progress indicators added for long sequences.\par -- Added local BLAST interface to main program interface (rather than \par just in sequence/alignment docs)\par -- The paste in the sequence edit box that caused it to go very slow \par with long sequences has been fixed (>500,000 residue pasting is no\par longer a problem). \par \par The following changes and/or fixes have been made since version v4.7.5:\par \par -- Fixed bug in link to ReadSeq that caused it to fail with long file\par names. \par -- Added Read-in filter for GCG format\par -- fixed small glich in sequence spacing control placement\par \par The following changes and/or fixes have been made since version v4.7.4:\par \par -- Fixed a few leftover bugs in the graphic shaded views (mostly spacing)\par -- user control over vertical spacing of sequences\par -- Added view of similarity scoring matrix files from doc windows\par -- edit titles on screen (highlight a title, then click it again)\par -- Fixed bug in local blastp -- matrix choices other than BLOSUM62 \par should work now\par \par The following changes and/or fixes have been made since version v4.7.3:\par \par -- A rich text export was added to the shaded graphic view utility. This\par uses the highlight command in the Rich Text Format specification 1.5,\par and is probably compatable only with relatively modern word-processors.\par -- Made a few changes and fixes to the shaded view. \par -- Added a "find in next title" function to the main document window\par -- Added a few normal and auomated web links \par \par The following changes and/or fixes have been made since version v4.7.2:\par \par -- Clustal format (.aln) filter was updated so it now compatible with\par the sequence numbers option in ClustalX\par -- A "delete numbers" option was put in under the sequence menu to allow\par easier compatability with copying and pasting from numbered formats\par -- In the shaded graphic view, an option to print lines continuously (not\par broken by a space every ten residues) was added\par -- An option to place translations below nucleotide sequences in either\par one-letter or three-letter format was added (allows for coloring with\par amino acid color table colors, but no similarity shading of the amino\par acids in this view).\par \par The following changes and/or fixes have been made since version v4.7.1:\par \par -- 8/27/1999: Added option for outlines around identity and similarity\par shading in shaded graphic view of alignments\par -- 8/27/1999: Fixed small bug in restriction maps. If more than one\par enzyme cut at the very position starting a new line on the printed \par map, only the first enzyme would show on the map (though all would \par appear in the lists). \par -- User options are provided for a (hopefully) more useful consensus\par sequence generation.\par -- The ABI trace viewer was updated to provide summary information and\par to allow copying of the trace window as a bitmap (in last version, \par I forgot to add that the option to copy print pages as Metfiles was\par also added).\par -- Support for reading Clustal format has been added (no save, only open).\par \par The following changes and/or fixes have been made since version v4.7.0:\par \par -- The graphic shaded view was improved. It's more like a print preview.\par Also, the option to add numbers to the sides of the sequences has been \par added.\par -- *Another* introduced bug was fixed in the accessory applications launch\par interface. This bug was preventing input and output file name command\par prefixes from being added to the command line (needless to say, many \par apps would not run"\par -- Font size control has been added to the single sequence editing box.\par -- Accessory apps no longer need to be run from an alignment doc unless\par they operate upon sequence output.\par \par The following changes and/or fixes have been made since version v4.6.3:\par \par -- Support for ABI chromatographs has been added. Display, zoom, scale,\par select, copy, export and reverse complement sequences from ABI trace \par files. Also print with professional-looking formatted color output \par similar to commercial output.\par -- Some memory leaks were fixed.\par \par The following changes and/or fixes have been made since version v4.6.2:\par \par -- Corrected 'Del' key behavior in edit residues mode and in single\par sequence edit interface\par -- Added sequence number to beginning of mouse position labels\par -- Fixed alignment of ruler ticks for non-type-set fonts\par \par The following changes and/or fixes have been made since version v4.6.1:\par \par -- Fixed a bug that caused simulataneous entry of characters into mutual\par information examiner X or Y entry and sequence when in Edit Residues\par mode\par -- Fixed glich that caused ruler to not extend to end of window in very\par high screen resolutions with small font size\par -- Fixed problem (I think) with disappearing window controls (minimize,\par maximize and close controls)\par \par The following changes and/or fixes have been made since version v4.5.10:\par \par -- Scroll a full screen at a time with the PageUp/PageDown keys and \par with Ctrl+arrow keys -- also refined cursor movement in edit mode\par and keyboard-controlled scrolling\par -- BioEdit now remembers your last window state as the default\par -- Fixed a bug in the single sequence edit window -- applying twice\par in a row after creating a new sequence no longer causes an access\par violation\par -- Improved speed of dynamic shading of protein alignments in the edit \par window \par \par The following changes and/or fixes have been made since version v4.5.9:\par \par -- Fixed bug in edit-window shading (maximizing window shouldn't cause\par a problem now).\par -- Added Select to End, Select to Beginning and Select Residues of \par Selected Sequences functions\par -- Changed open and save file dialogs to remember file extensions\par and last directory as defaults\par -- Added recent file list to the file menu\par -- Added function to open an edit box at the current cursor position\par (when in Edit Residues mode) \par -- Added Tile and Cascade window functions\par \par The following changes and/or fixes have been made since version v4.5.8:\par \par -- Added identity/similarity-based shading in the alignment window\par -- Fixed a bug in the matrix plotter which caused it to periodically\par crash when plotting a half matrix (above diagonal only).\par -- Fixed bug in N-best reporting of mutual information and N-best and \par P-best reports when data are organized for the whole alignment rather\par than by position (I forgot that those things had never been finished).\par \par The following changes and/or fixes have been made since version v4.5.7:\par \par -- Added information-based searching for conserved segments (may be \par useful for designing PCR primers or defining motifs)\par -- Made the sequence titles window adjustable in width\par -- Fixed bug in six-frame translations: An "N" in the sequence no \par longer causes an amino acid to be skipped\par -- Added a "Minimize Alignment to Mask" function to allow trimming\par an alignment to positions present in a mask sequence\par -- Added positional numerical summary for nucleotide alignments\par -- Changed entropy plots to area plots that resize with the window\par -- Added a full-text summary of entropy (Hx) values when an entropy\par plot is run \par -- Got rid of the "three-way information" thing (too much noise to be\par useful)\par \par \par The following changes and/or fixes have been made since version v4.5.6:\par \par -- The vertical split has been improved -- no longer flickers wildly \par when going between windows (also, no longer "left" and "right" \par panes -- it's just one window now). The horizontal split view is\par still not-so-great.\par -- Added option to hide panels for controls at top (to allow for a bigger\par sequence editing window)\par -- Sped-up right-click driven insertions and deletions. Added option\par to reverse mouse buttons (to allow inserting and deleting gaps with\par a left click)\par -- Fixed glich in window updating when switching between color and B&W\par -- Fixed glich in translations on restriction maps -- spacing was off if\par an "X" resulted from a codon with a non-A, C, G or U/T character.\par -- Added menu items for all button-driven controls\par -- "Lock gaps" no longer causes an error when residue selection goes \par beyonf the end of a sequence.\par \par \par The following changes and/or fixes have been made since version v4.5.5:\par \par -- Fixed bug in residue selecting that was introduced with the sequence\par handling rewrite: The location of a selected block of residues was\par not scrolling correctly in the horizontal direction\par -- Changed the way the matrix plotter draws matrices. The speed is\par improved several hundred fold. \par -- Added threshold control to matrix plotter.\par \par The following changes and/or fixes have been made since version v4.5.4:\par \par -- Fixed glich in amino acid composition reporting -- previously, non-\par amino acid characters were assigned a mass of 110 Da. Now, only 'X'\par is assigned 110, other characters are 0 Da (not counted as amino \par acids). The weight of 'B' is considered the average of 'D' and 'N',\par and the weight of 'Z' is the average of 'E' and 'Q'. Also, a stop \par codon at the end of a sequence no longer adds 1 amino acid to the\par reported length of the sequence.\par -- A couple of changes were made to the accessory application \par configuration interface and the way accessory apps are run:\par 1. Options to include or not include the input and output files in\par the command line were added, as well as the option to include\par them at the beginning or end of the command line.\par 2. changed the method of calling accessory apps: redirection of \par stdin and stdout now *appears* to work correctly in all cases\par The few PHYLIP programs distributed with BioEdit now have stdin\par redirected so they may be run fully automated.\par -- Forgot to report in an earlier version: a bug in converting selected\par regions to lowercase was fixed (left out 'A')\par \par The following changes and/or fixes have been made since version v4.5.3:\par \par -- The on-line help system was updated (the printable documentation \par still needs updating -- also the WWW documaentation needs to be \par updated (don't know when that'll get done)).\par -- Fixed a bug in resizing split windows (introduced with version \par 4.5.3 -- would cause an exception when the window was increased \par vertically due to an oversight in creating a new graphic sequence\par display object).\par \par The following changes and/or fixes have been made since version v4.5.2:\par \par -- Sequence handling and memory allocation for sequences was re-written. \par Alignments load much faster and editing of large alignments is more \par reasonable. When using the new BioEdit Project file format, the \par prokaryotic 16S rRNA alignment (6205 sequences, 29 Mb file) opens in \par less than 10 sec. on a Pentium 233 MHz with 80 Mb RAM. \par -- Created a new binary file format (the BioEdit Project file) for fast \par Open and Save of large alignments.\par -- A bug in formatting when exporting an aligment as raw text was fixed \par (the spacing would be randomly messed up -- this bug was introduced \par with version 4.3.8 and was only recently discovered because this \par feature apparently does not get used much). \par -- Two bugs in the vertical split window view were fixed: \par 1. When the original window's vertical scrollbar was not at the top, \par the right side of the split window would start out of register \par with the left side.\par 2. The left side of the window would not scroll all the way to the \par end.\par -- A couple of changes to the sequence edit box:\par 1. The first digit of ruler positions >1,000,000 is no longer deleted\par from the ruler bar.\par 2. The "Delete" key now works in the edit box as well as "Backspace"\par -- A typo on the vertical axis of Eisenberg mean hydrophobic moment plots\par was fixed.\par -- Changes to matrix plotter:\par 1. Clicking on the plot when there is no 1-D line plot open no longer \par crashes the program\par 2. Highlighting of the selected matrix position on the plot has been\par fixed (the selected position is inverted and outlined).\par 3. The data summary reported for a highlighted matrix position reflects\par the position numbers in the matrix file rather than the absolute \par row or column number (x and y position numbers may be discontinuous,\par as when alignment numbering is used to generate the Mxy data or when\par a numbering mask different from the sequence mask is used).\par 4. The row or column numbers shown on the 1-D matrix row/column plots \par reflect the position numbers in the matrix file.\par 5. A bug in reporting of the current row or column that showed up when an\par asymmetric section of a matrix file was plotted has been fixed (if a \par matrix contained more rows than columns, row numbers beyond the total\par number of columns would be mis-reported).\par -- "Flags" are now available to graphically mark any position in an alignment\par for keeping track of positions while when going back and forth a lot.\par -- The sequences have been crunched together slightly for a tighter view with \par more sequence data on the screen at once.\par -- User may enable or disable position reporting at the mouse arrow.\par \par \par The following changes and/or fixes have been made since version v4.5.1:\par \par -- Added option to translate selected regions of nucleic acid sequences\par for formatted translation with codon summary, with the option to \par display the entire nucleic acid sequence or only the translated region\par -- Added option for single-letter or three-letter codes for amino acids\par in formatted translations\par -- Fixed a couple of bugs related to non-U.S. versions of Windows: errors\par resulting from the difference between U.S. and European decimal separators\par (period vs comma) have been fixed in the text print, RNA anaylises outputs,\par the matrix plotter, and formatted translations. \par -- Updated matrix plotter to provide a summary of matrix dimensions before\par loading up a matrix, and added the capability to plot user-defined regions\par of matrices. The plotter can now handle a nearly unlimited matrix size (but\par can still only plot ca. 1500 x 1500 (maybe up to about 2000 x 2000) at one\par time. The largest file tested was 179 Mb (5183 x 5183).\par -- Expanded sequence limit to 10000 (sequence size is limited only by system \par resources and speed). \par \par The following changes and/or fixes have been made since version v4.5.0:\par \par -- Vertical split window view was added\par -- About 16 billion bugs were fixed in the split window view synchronization\par \par The following changes and/or fixes have been made since version v4.4.2:\par \par -- Improved shaded views: added color table-based shading, shading with\par sequences in color, and improved Metafile copying\par -- New sequence edit box, with sequence view, ruler and color\par -- Added ORF searching (under Nucleic Acid submenu of Sequence menu)\par -- Added split window option for simultaneous editing of two different \par places in the same file\par \par The following changes and/or fixes have been made since version v4.4.1:\par \par -- blastx was added to the local BLAST interface\par -- Image Export (Bitmap or Windows Metafile) added to plasmid utility\par with variable output size options\par -- Clipboard copy as a Windows Metafile added to plasmid utility and\par to shaded graphic view utility\par \par \par The following changes and/or fixes have been made since version v4.4.0:\par \par -- Fixed "Cut" and "Copy" options for working with linked \par nucleotide/protein views.\par -- Added user control over menu shortcuts in alignment documents\par (to customize shortcuts, go to "Customize Menu Shortcuts" from\par the "View" menu)\par -- Added "Auto-Update View Options" item under the "View" menu -- \par when checked, the "Save Options as Default" item is not visible,\par and view options are automatically saved whenever a change is\par made\par -- Added multiple file handling for opening and importing files\par -- Fixed redraw of ends of sequences when in a non-typeset font.\par \par \par The following changes and/or fixes have been made since version v4.3.10:\par \par -- Fixed bug in translating and translation toggling (no longer\par bombs out after several translations)\par -- Non-typeset font handling was improved for the editing window\par and in graphic shaded view\par -- Read filters for NBRF/PIR and Phylip 4 formats were improved\par -- Monochrome sequence view fixed (can't remember when or how\par I broke it -- but it got broken).\par -- Three options were added for handling gaps for translating\par when toggling between nucleotide and protein views:\par 1. gaps automatically adjusted to occur in groups of three\par that do not disrupt codons\par 2. gaps that disrupt codons or do not occur in groups of \par three may be ignored in trnaslating, but no automatic\par adjustment of gaps\par 3. No automatic adjustments to gaps made, and gaps not\par ignored when translating \par \par \par The following changes and/or fixes have been made since version v4.3.9:\par \par -- Two bugs that were introduced into version 4.3.9 were fixed:\par 1. Access Violation that would occur after previewing "Print \par Alignment as text"\par 2. Access Violation that would occur upon running mutual \par information analysis\par \par * These two bugs only occurred in version 4.3.9 *\par \par \par The following changes and/or fixes have been made since version v4.3.8:\par \par -- The program was restructured internally to use less memory and much \par fewer system resources. As a result, the program loads much faster \par and is not as demanding of the operating system. If you have \par experienced any trouble with starting BioEdit, this may solve the \par problem.\par -- Two bugs were fixed in the display of selected residues:\par 1. The entire selection is now highlighted correctly in very \par long stretches of selected residues (more than ca. 25000 \par residues).\par 2. When selecting entire columns by selecting on the sequence\par position ruler, the selection highlighting would sometimes\par get broken, with some selections not appearing highlighted.\par This has been fixed. \par \par The following changes and/or fixes have been made since version v4.3.7:\par \par -- Added click-select capability fo viewing data points in the matrix \par plotter\par -- When creating a line graph from matrix data, the row selected on \par the matrix plotter is graphed\par -- When toggling between row and column views in matrix row/column\par graphs, the selected data point on the matrix plotter is used\par -- When rows or columns are scrolled through on a line graph, the \par selected data point on the matrix plotter (if there is one) is \par updated to match\par -- Rows or column may be selected for an open matrix line graph by\par selecting a point on the matrix plotter.\par -- Fixed a bug in memory allocation for the matrix plotter: The last\par point of the matrix no longer disappears\par -- Matrix table reading is now more flexible (It can handle \par inappropriate spaces, tabs or returns in the file without giving\par an error)\par -- Matrix plotter now read .csv (comma-delimited) matrices as well as\par tab-delimited\par -- A bug was fixed for updating feature titles in the plasmid drawing\par utility: The updated title is selected and sized correctly on the \par screen now\par -- Linear vector maps should now shade better on a grayscale laser\par printer (only circular maps were fixed previously)\par -- Moving the ends of horizontal or vertical arrows in the plasmid \par drawing utility now works correctly (doesn't get stuck horizontal \par or vertical anymore)\par -- A bug in the new nucleotide/protein translation view toggling was\par fixed: Previously, if gaps were accidentally introduced into the last \par codon of a nucleotide sequence and several gaps also occurred at the \par end of the sequence, an error would occur when BioEdit attempted to\par readjust gaps to mend codons. This should no longer be a problem\par \par \par The following changes and/or fixes have been made since version v4.3.6:\par \par -- The on-line help was updated with a full searchable index and full-\par text search capability\par -- Nucleotide sequences which encode proteins may be switched between \par their protein and nucleic acid sequences, and alignments may be \par edited in either view\par -- Simple translations of nucleic acids and reverse translations of \par proteins now take gaps into account rather than treating them as \par unknown residues\par -- ClustalW may now be run without modifying sequence titles to be \par non-redundant and 10 or few characters long\par -- When ClustalW is run from the accessory menu, the new alignment is \par automatically updated with GenBank information (features, references, \par accession, etc.) and full titles\par \par \par The following changes and/or fixes have been made since version 4.3.5:\par (These changes were both made to the plasmid drawing utility)\par \par -- Grouped drawing objects now scale as a unit\par -- Changed feature drawing to be more compatible with most printers\par \par \par The following changes and/or fixes have been made since version 4.3.4:\par (These changes were all made to the plasmid drawing utility)\par \par -- Added linear vector capability\par -- Made titles selectable and editable\par -- Made vector structure selectable and mouse-movable\par -- All objects and labels move along with vector when moving by hand\par -- Restriction sites and feature labels locations adjust themselves\par when vector is resized\par -- Bug fixed in plasmid utility: selecting multiple restriction site\par labels then hitting "delete" was causing trouble with the enzyme-label\par links\par \par \par The following bug fix has been made since version 4.3.3:\par \par -- A bug in the positioning of restriction cut sites at the origin \par junction of circular DNA sequences was fixed. This error occured\par when running a map on circular sequences that had a restriction site \par that overlapped the origin and cut after the overlap point. This would\par cause an error also when generating a plasmid map from such a sequence.\par \par \par The following changes and/or fixes have been made since version 4.3.2:\par \par -- Only one change: The sequence editing box now behaves better, and there\par is no set limit on the size of the sequence that can be opened and \par edited in an edit box (well, actually the theoretical upper limit is\par 10 million bases, but that would be too slow to be worth it, anyway).\par -- The printable documentation has been updated (It's only available for\par MS Word'97 or later).\par \par \par The following changes and/or fixes have been made since version 4.3.1:\par \par -- An incorrect value was corrected in the Kyte and Doolittle hydrophobicity \par data (valine was set at -4.2 instead of 4.2).\par -- Arrows were added to plasmid drawing interface\par -- Enzyme marks automatically follow their labels\par -- linking of enzyme sites to their labels seems to work well now (if an\par enzyme label is deleted, the site is taken off the map)\par -- Arrow heads on features automatically scale down in length when \par the feature is short\par -- Print scale problem has been fixed for plasmid drawing\par \par The following changes and/or fixes have been made since version 4.1.1:\par \par -- Modified hydrophobicity plotting to conform to Kyte and Doolittle mean \par hydrophobicity profile.\par -- Added file save and open capability for plasmid drawing files\par -- Added direct print for plasmid drawings\par -- Added object property editing for plasmid drawing\par -- Added copy and paste functions for plasmid drawing and modified \par copy to allow copying objects as bitmaps for pasting into other apps\par -- Added object ordering support in plasmid drawing utility\par \par \par The following changes and/or fixes have been made since version 3.1.4:\par \par -- Several bug fixes and improvements in plasmid drawing utility. This still\par has a long way to go\par \par The following changes and/or fixes have been made since version 3.1.2:\par \par -- Added new graphical plasmid drawing and annotation program\par -- Fixed graphc alignment view (no system crash on multiple pages\par anymore -- also made it more efficient)\par \par The following changes and/or fixes have been made since version 3.1.1:\par \par -- Fixed bugs in opening of Fasta files from Mac or UNIX format (was losing\par the first line of sequence)\par -- Fixed minor bug in opening of NBRF/PIR sequences (spaces in the title would \par truncate the title and tack extra characters at the beginning of the sequence\par -- Fixed color matching between series lines and legend of hydrophobicity plots\par -- Added scrolling/keyboard control of row/column number in line plots of\par mutual information matrix data\par \par \par The following changes and/or fixes have been made since version 2.0.4:\par \par -- fixed bug in LOCUS field of GenBank files (was duplicationg part of the LOCUS in\par some cases\par -- Better handling of Macintosh-formatted GenBank files\par -- Automatic scrolling in Grab and Drag mode.\par -- arrow key control over window scrolling\par -- added horizontal scroll speed controller\par -- Fixed information-responsive residue shading (capital/lowercase residues no longer seen\par as different, and multiple gaps now reduce the alignment strength rather than increase it)\par -- Uppercase/lowercase, lock/unlock and degap control of sequence selections as well as \par complete sequences.\par -- Added zoom capabilities to RNA data matrix plots\par -- Added Single-row plotting for individual rows of data matrices, with the option to\par print graphs or copy as Bitmap, Metafile or Enhanced Metafile.\par -- Added capability for three-way information analysis (doesn't seem to be very worthwhile, however).\par -- Fixed font handling in edit window to allow proper scaling of any font\par -- Added hydrophobicity/hydrophilicity profile plotting for proteins\par -- Added nucleotide and amino acid composition summaries and plots\par -- Added codon-parsed translation and codon-usage summaries for all three \par frames of nucleotide sequences\par -- Reorganized some of the "Sequence" menu, now with separate protein and\par nucleic acids submenus\par -- Added selection of restriction enzymes by manufacturer and reporting of \par manufacturers that carry each enzyme\par -- Updated restriction enzyme table to gcgenz.811, from REBASE version 811 (Oct 28 98)\par (added to BioEdit Nov 3 98) \par \par ---------------------------------------------------------------------\par \par How to contact the author:\par \par Tom Hall\par 760-201-6089\par tomandhall@gmail.com\par \par }

thalljiscience / thalljiscience.github.io

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