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README

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 <Mode> <options> <sequence_file>

$ phylosift <Mode> <options> --paired <sequence_file_1> <sequence_file_2>

   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
<test.aln>, the marker name will be <test>


== Index the search databases ==

This step is run automatically when markers are downloaded but if you
add new markers, you will need to run this step manually.

`phylosift index`


== Modes ==


      commands: list the application's commands
          help: display a command's help screen

         align: align homologous sequences identified by 'search'
           all: run all steps for phylogenetic analysis of genomic or metagenomic sequence data
     benchmark: measure taxonomic prediction accuracy on a simulated dataset
  build_marker: add a new marker the reference database based on a sequence alignment
      dbupdate: update the phylosift database with new genomic data
         index: index a phylosift database after changes have been made
          name: Replaces phylosift's own sequence IDs with the original IDs found in the input file header
         place: place aligned reads onto a reference phylogeny
        search: search input sequence for homology to reference gene database
      simulate: simulate sequencing from a metagenomic sample
     summarize: translate a collection of phylogenetic placements into a taxonomic summary
  test_lineage: conduct a statistical test (a Bayes factor) for the presence of a particular lineage in a sample
                    
== Requirements ==

PhyloSift requires a 64-bit operating system. PhyloSift will NOT work
on a 32bit operating system. PhyloSift depends on a great many other
open source software packages. The precompiled version linked above
bundles most of the dependencies into a single downloadable package.

== Results ==

Results are saved to the path specified with the --output option.
If no path is given, the default location for results is `PS_temp/<filename>/`.

*  blastDir : All files related to the search step.  

     *  *.candidate.aa.*      Fasta format of the candidate sequences in
                        Protein space for each marker 

     *  *.candidate.ffn.*  Fasta format of the candidate sequences in DNA
                        space for each marker (option activated)

*  alignDir : All files related to the alignment and masking steps.

     *  *.newCandidate.*   Fasta file of the candidate sequences 
                           copied from the blastDir
     *  *.fasta            hmmer3 generated alignment for the 
                           candidate sequences in fasta format
     *  *.codon.*.fasta    reverse-translated alignment of DNA
     *  *.unmasked 	       The unmasked sequence of homologs that aligned
                           successfully and passed all filter thresholds 

*  treeDir : Files containing placements of sequences onto reference
              phylogenetic trees

     *  *.jplace            Phylogenetic placements of the aligned sequences
     *  *.codon.*.jplace    Phylogenetic placements for codon alignments

*  taxasummary.txt        Probability mass over taxa present in the sample,
                          tab-delimited text

		Column 1 -- NCBI Taxon ID
		Column 2 -- Taxonomic rank (genus, species, phylum, etc)
		Column 3 -- Name
		Column 4 -- Read/sequence probability sum placed at this taxon
                  The values in this column can be normalized to sum to 1,
                  the result will be a rank-abundance distribution

== SUPPORT AND DOCUMENTATION ==

After installing, you can find documentation for this module with the
perldoc command.

    perldoc Phylosift::Phylosift

Bugs and other apparent problems with the software can be reported as
issues in our github issue tracker :

   https://github.com/gjospin/PhyloSift/issues

== LICENSE AND COPYRIGHT ==

Copyright (C) 2011 Aaron Darling and Guillaume Jospin

This program is free software; you can redistribute it and/or modify it
under the terms of either: the GNU General Public License as published
by the Free Software Foundation.


== 3rd PARTY SOFTWARE ==

PhyloSift is distributed with several open source components that were developed by other groups.
These components are (c) their respective developers and are redistributed with PhyloSift to provide ease-of-use.

Please see the following web sites for licensing details and source code for these other components:
* pplacer -- http://matsen.fhcrc.org/pplacer/
* HMMER 3 -- http://hmmer.janelia.org/
* LAST -- http://last.cbrc.jp
* pda -- http://www.cibiv.at/software/pda/
* FastTree -- http://www.microbesonline.org/fasttree/
* infernal -- http://infernal.janelia.org/

The above list is not exhaustive.

== CONTACT INFORMATION ==

Please direct correspondence to aarondarling (at) uc davis (dot) edu
Or on twitter to @PhyloSift
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