PhyloSift

PhyloSift is a suite of software tools to conduct phylogenetic analysis of genomes and metagenomes.

Using a reference database of protein and RNA sequences, PhyloSift can scan new sequences against that database for homologs and identify the phylogenetic relationship of the new sequence to the database sequences. During this procedure, high quality alignments of codon and amino acid sequence are generated.

Website : http://phylosift.wordpress.com/ Twitter : @PhyloSift

User support forum: https://groups.google.com/d/forum/phylosift Our google group is a place to ask questions, request functionalities, get help if you're stuck, and generally interact with our development team at UC Davis.

Please report software errors and bugs as issues in our github tracker: https://github.com/gjospin/PhyloSift/issues All known bugs are documented in the issue tracker and marked with their resolution status.

== Quick Start for the Impatient ==

Download PhyloSift from here: http://edhar.genomecenter.ucdavis.edu/~koadman/phylosift/phylosift_latest.tar.bz2

Unpack with tar xvjf phylosift_latest.tar.bz2, then change into the new directory and run:

bin/phylosift all --output=results sequences.fasta

Or using compressed paired FastQ data from an Illumina instrument:

bin/phylosift all --output=results --paired read_1.gz read_2.gz

Results will be stored in a new directory called "results".

See results/sequences.fasta.html for a visual summary of the sequence data. Run javaws results/sequences.fasta.jnlp to browse a phylogeny with branches thickened by relative abundance in the sample.

== Detailed installation instructions ==

The easy way :

Download the tarball archive from

http://edhar.genomecenter.ucdavis.edu/~koadman/phylosift/phylosift_latest.tar.bz2

Navigate to the directory where you downloaded the software and run :

tar -xvf phylosift_latest.tar.bz2

PhyloSift is ready for use. Refer to the Usage section.

The hard way (installing from the development repository) :

Download and install Git for your system.

http://git-scm.com/

For debian/ubuntu systems, run the following command

sudo apt-get install git

To check out the PhyloSift development repository, run the following command :

git clone git://github.com/gjospin/PhyloSift.git

It may also be necessary to install several support packages, including BioPerl, Bio::Phylo, and others. BioPerl offers bioperl-live from github, we suggest installing other dependencies using cpan.

== Dependency software ==

PhyloSift depends on a number of external software modules, including BioPerl, Bio::Phylo, LWP::Simple, and others. We have attempted to package these dependencies with phylosift but every operating system is unique and there may be system-specific requirements that are not met. If you see messages from the perl interpreter suggesting that a module is missing, we suggest using the cpan system to install the missing dependency.

To run build_marker mode, the installation of taxit and its dependent python modules (e.g. SQLAlchemy) is required. taxit is available from: https://github.com/fhcrc/taxtastic

== Updating PhyloSift ==

If running PhyloSift from a packaged release (i.e., you chose the "easy way"), simply download the newest tarball.

If running PhyloSift from the development repository, run the following command :

git update

== Usage ==

PhyloSift currently accepts input data in the following file formats:

• FASTA
• paired FASTA (specify paired data by using the --paired flag)
• interleaved paired FASTA (specify paired data by using the --paired flag)
• FASTQ (same as FASTA but with quality scores; this file type is the standard output from Illumina platforms)
• interleaved FASTQ (same as FASTA but with quality scores)
• .gz (any of the above file types compressed using gzip)
• .bz2 (any of the above file types compressed using bzip2)

PhyloSift can be executed by running the following command:

$ phylosift

$ phylosift --paired

sequence_file_1 and _2 must contain paired sequences

Creating a PhyloSift marker :

Example 1: phylosift build_marker -f --alignment=test.aln --reps_pd=0.01

Example 2: phylosift build_marker -f --alignment=test.aln --taxonmap=test.taxonmap

The new marker will be added directly to the phylosift marker database.

NOTE : This step does not automatically add the new marker to the search databases. You will need to run phylosift index after building a marker.

If a marker with the same name already exists, the marker build process will be halted unless the -f or --force option is used.

The marker name will be the same as the alignment given minus the trailing suffix. If the user wants to build a marker from the file