Phylogenetics

Python scripts for phylogenetics. This is mainly work on creation of trees and super trees, and some utilities related with them. Phylogenetic building need appropriate software, so this is not intended for tree buiding, but more to glue techniques. It ONLY WORKS RELIABLY IN LINUX SYSTEMS!!!!! Feel free to change all paths, end of line characters, etc.. to make it work on others (Yes, i did not use os.path modules to make it happen).

It contains:

GarliRunner.py:

This script will iterate over fasta files in a given directory, create the garli.conf and run garli for each gene. Each Fasta file should be an alignment for each gene.

It requires:

1. Garli
2. JModelTest or ProtTest
3. if in a cluster passTosub.py available from Alex Safatli at https://github.com/AlexSafatli/LabBlouinTools

mergeFasta.py:

This script will get two or more .fasta files and its corresponding SpList.txt and merge them. This is useful when SeqFetcher.py creates two files with different names, but that refers to the same gene (i.e. cytb and cytochrome b). It requires a SpList.txt which is a file linking a species name with all accession numbers downloaded. It is of the form:

Species1: Accesion1, Accesion2, ... , Accession_n
Species2: Accesion1, Accesion2, ... , Accession_n
.
.
.
Speciesn: Accesion1, Accesion2, ... , Accession_n

The fasta file should have the .fas extension and should contain the species name and accession as sequence header like:

Species1_accesion1 SEQUENCE BIT Species1_accession2 SEQUENCE BIT Species2_accession3 SEQUENCE BIT . . .

This files are also created by SeqFetcher.py, freely available in this repo.

multi2single.py:

This Script allows you to collapse multiple species into a single leaf. It will return a file with a list of unique names, a csv file with Species,gene,type, Accession, and Source (the last one if the format is apropriate), and a new tree with "collapsed" leafs. This script assumes that you have a bunch of tree files in newick format with the extension .tree, and the name must follow _ where gene is the label for the given marker and type is the label for the type of data (either prot for protein or nuc for nucleotide). Requires:

1. Dendropy available at http://pythonhosted.org/DendroPy/

properAlignment.py:

This script will go over the files created by SeqFetcher.py and will execute translatorX on the coding sequences, giving the apropriate genetic code. For non-coding or RNA, will use muscle. Requires:

1. Biopython
2. translatorx.pl available at http://pc16141.mncn.csic.es/cgi-bin/translatorx_vLocal.pl
3. perl
4. muscle available at http://www.drive5.com/muscle/

SeqFetcher.py:

This script will get the sequences from NCBI. Read the NCBI code of conduct before. This script will return a set of files of unaligned ([].fas) and aligned ([].fasta, if specified) sequences for a given search. It also return a list of species and a pickled file (GenesnSpecies.pckl), if the program crash in the writing part. Requires:

1. Biopython

SuperMatrix.py:

This script will go over the fasta files created by SeqFetcher (or at least in the same format), will create new fasta files with consensus sequences per species and transform them to nexus using Joseph Hughes (University of Glasgow) Consensus.pl and Fasta2Nexus.pl, respectively. by , concatenate all the sequences using the 'NEXUS' module of biopython ('NEXUS: An extensible file format for systematic information' Maddison, Swofford, Maddison. 1997. Syst. Biol. 46(4):590-621, and will launch a RAxML (Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22(21), 2688-2690.) either in fester (a private cluster) or locally.

Requires:

1. Consensus.pl, which in turn requires BioPerl libraries. Available at
   http://www.vcu.edu/csbc/bnfo601/Scenarios/Blast/consensus.pl
2. Biopython
3. Fasta2Nexus.pl, which in turn requires BioPerl libraries
4. RAxML, available at http://sco.h-its.org/exelixis/web/software/raxml/index.html
5. perl available at http://raven.iab.alaska.edu/~ntakebay/teaching/programming/perl-scripts/fasta2nexus.pl
6. A utils folder available at https://github.com/AlexSafatli/LabBlouinTools

Points 1,3 should be in the same folder of the selected fasta files. The requirement 6 should be either in the same folder or in the python path