lonelyjoeparker qmul-genome-convergence-pipeline issues

lonelyjoeparker / qmul-genome-convergence-pipeline

API and binaries for phylogenomic analyses, particularly comparison of input trees/alignments (CONTEXT) and detecting genomic convergence

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issues

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ResultsPrinterSimple - column header definitions

#61 lonelyjoeparker closed 6 years ago
0
PAML filename I/O still not stable

#60 lonelyjoeparker opened 7 years ago
2
Parse nexus treefiles

#59 lonelyjoeparker closed 7 years ago
1
Phylogeny view stats rendering

#58 lonelyjoeparker closed 7 years ago
1
Implement remaining tree stats

#57 lonelyjoeparker closed 7 years ago
0
overlay CONTEXT plots

#56 lonelyjoeparker opened 7 years ago
0
Save plots as image

#55 lonelyjoeparker opened 7 years ago
0
Track alignment pane position between AA and NT windows.

#54 lonelyjoeparker closed 7 years ago
0
Add system hotkeys for common functions

#53 lonelyjoeparker closed 7 years ago
1
Add Charting -> XChart

#52 lonelyjoeparker closed 7 years ago
2
Optimise ASR

#51 lonelyjoeparker opened 7 years ago
0
ASR imports - duplicate taxon names not processed correctly

#50 lonelyjoeparker opened 8 years ago
1
Implement cods through readthedocs for public beta

#49 lonelyjoeparker opened 8 years ago
0
x-pos in Alignment panes - flipping between alignments

#48 lonelyjoeparker opened 8 years ago
0
PAUP sequences not parsing correctly

#47 lonelyjoeparker opened 8 years ago
1
Phylogeny statistics

#46 lonelyjoeparker closed 7 years ago
2
Phylogeny display rendering problems/slowness

#45 lonelyjoeparker closed 9 years ago
1
Phylogeny display from multiple-phylogeny files seems to have too many tip labels

#44 lonelyjoeparker closed 9 years ago
1
Feature list / tweaking bugs for phylogenomic dataset browser 0.9 release

#43 lonelyjoeparker closed 7 years ago
3
AlignedSequenceRepresentation.translate() doesn't cover all codons

#42 lonelyjoeparker closed 7 years ago
0
AA alignment stats identical to NT stats for entropy, gapped lengths etc

#41 lonelyjoeparker closed 9 years ago
1
GCP: Add text export of alignment stats and convergence results

#40 GoogleCodeExporter opened 9 years ago
1
Add JScrollPane to phylogeny view

#39 GoogleCodeExporter closed 9 years ago
3
NEXUS files authored by mesquite are not parsing correctly

#38 GoogleCodeExporter opened 9 years ago
1
Table data for analyses and results and alignments

#37 GoogleCodeExporter opened 9 years ago
1
Correct table header widths

#36 GoogleCodeExporter closed 7 years ago
0
Inconsistent file paths for local files in GUI setup

#35 GoogleCodeExporter opened 9 years ago
3
SiteSpecificLikelihoodSupportAnalysis doesn't check for non-null input arguments

#34 GoogleCodeExporter closed 9 years ago
2
New requests viewer

#33 GoogleCodeExporter opened 9 years ago
0
AlignedSequenceRepresentation clone() method is not safe

#32 GoogleCodeExporter opened 9 years ago
0
GeneralCongruenceRunnerXML (r212) :80 - models hardcoded

#31 GoogleCodeExporter opened 9 years ago
0
Float NumberFormatException: multiple digits when parsing codeml rst files

#30 GoogleCodeExporter opened 9 years ago
0
Feature request - NewickTreeRepresentation tip labelling

#29 GoogleCodeExporter closed 9 years ago
2
CodemlRstParser - requirement to parse sitewise omegas differently

#28 GoogleCodeExporter opened 9 years ago
1
CodeML C parsing error

#27 GoogleCodeExporter opened 9 years ago
2
selected site aggregation analysis bug

#26 GoogleCodeExporter closed 9 years ago
2
CodemlRstParser - heap space error

#25 GoogleCodeExporter closed 9 years ago
1
ResultsPrinterSimsCDF - java.lang.IllegalArgumentException arising from format call BigDecimal - uk.ac.qmul.sbcs.evolution.sandbox.ResultsPrinterSimsCDF.go2(ResultsPrinterSimsCDF.java:654)

#24 GoogleCodeExporter closed 9 years ago
1
Phylip files written with original names cannot be read by PAML

#23 GoogleCodeExporter closed 9 years ago
2
Uncaught IllegalArgumentException in ResultsPrinterSimsCDF.go2() method

#22 GoogleCodeExporter opened 9 years ago
0
ResultsPrinterSimple - large memory footprint and long start-up time

#21 GoogleCodeExporter opened 9 years ago
0
ResultsPrinterSimple - output hard to understand

#20 GoogleCodeExporter opened 9 years ago
0
Arguments to GeneralCongruencePipelineXML missing: noninformative die

#19 GoogleCodeExporter opened 9 years ago
0
Training binary fails to call external libs

#18 GoogleCodeExporter opened 9 years ago
0
# taxa issue - AA frequencies matrix incorrectly initialised

#17 GoogleCodeExporter opened 9 years ago
0
detection of locus identity in serialised results files (uk.ac.qmul.sbcs.evolution.convergence.util.SitewiseSpecificLikelihoodSupportAaml)

#16 GoogleCodeExporter closed 9 years ago
1
Translation of codons with missing data

#15 GoogleCodeExporter closed 9 years ago
2
CDF bin discretizations

#14 GoogleCodeExporter closed 9 years ago
1
Error in likelihood fit for prestin (alternative) tree on prestin-simulated data

#13 GoogleCodeExporter closed 9 years ago
1
AU - test

#12 GoogleCodeExporter opened 9 years ago
0