LANL-Bioinformatics/PhaME

Name: PhaME

Owner: LANL-Bioinformatics

Description: Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (genes under positive selection) using CDS SNPs.

Forked from: sanahmed/PhaME

Created: 2015-08-30 14:12:17.0

Updated: 2017-06-07 17:55:21.0

Pushed: 2017-08-21 16:41:47.0

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Size: 1023

Language: Perl

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README

Phylogenetic and Molecular Evolution (PhaME) analysis tool

Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (genes under positive selection) using CDS SNPs.

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Version

1.0

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SYSTEM REQUIREMENTS

• Perl version >5.8

• MUMmer version 3.23 - Pairwise alignment using NUCmer

• Bowtie version >=2.1.0 - Mapping of reads

• SAMtools version 0.1.19 and vcftools - Convert BAM files created by Bowtie

• FastTree version >=2.1.8- Contruction of phylogenetic tree

• RAxML version >=8.0.26 - Maximum likelihood construction of phylogenetic tree

• mafft version >=7.0 - For optional evolutionary analyses

• pal2nal version >=14 - For optional evolutionary analyses

• paml version >=4.8 - For optional evolutionary analyses

• HyPhy version >=2.2 - For optional evolutionary analyses

The C/C++ compiling enviroment might be required for installing dependencies. Systems may vary. Please assure that your system has the essential software building packages (e.g. build-essential for Ubuntu, XCODE for Mac…etc) installed properly before running the installing script.

PhaME was tested successfully on our Linux servers (Ubuntu 14.04.3 LTS).

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Obtaining PhaME

You can use “git” to obtain the package:

$ git clone https://github.com/LANL-Bioinformatics/PhaME.git

Installing PhaME

$ cd PhaME
$ ./INSTALL.sh

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Running PhaME

Prepare the input files

INPUT files required

• A directory with reference files which have the following file suffixes

• *.fasta

• *.fna

• *.fa

• *.gff (optional: to analyze Coding region SNPs of a selected reference file)

• A working directory

• Contig files with the following file suffixes

  • *.contig
  • *.ctg
  • *.contigs

• Reads files with the following file suffixes

  • *R1.fastq *R2.fastq
  • *R1.fq *R2.fq

• A control file (e.g. phame.ctl)

Test run

• Please modify the values of 'refdir' and 'workdir' in the test/phame.ctl file to corresponding absolute PhaME installed path.

• From the PhaME directory

  $ bin/runPhaME.pl test/phame.ctl

OUTPUT files

• Summary

• A SNP alignment file

• A newick tree file

• Text file containing the size of gaps, the core genome size, the average genome size, number of whole genome SNPs, and coding region SNPs.

• A pairwise list of all SNPs and coordinates between references and samples

• A matrix file that lists the number of SNPs present between genomes

• Directories structure

• working directory/files

  • permutated versions of references (concatenated chromosomes)

• working directory/results

  • All output files generated

• working directory/results/snps

  • SNP coordinate files generated from NUCmer and Bowtie

• working directory/results/gaps

  • Gap coordinate files generated from NUCmer and bowtie

• working directory/results/stats

  • Intermediate stat files generated when parsing NUCmer and Bowtie results

• working directory/results/temp

  • Temporary files generated

• working directory/results/PSgenes

  • All gene fasta files that contain at least 1 SNP

• working directory/results/paml

  • PAML results

• working directory/results/hyphy

  • HyPhy results

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CITATION

From raw reads to trees: Whole genome SNP phylogenetics across the tree of life.

Sanaa Afroz Ahmed, Chien-Chi Lo, Po-E Li, Karen W Davenport, Patrick S.G. Chain

bioRxiv doi: http://dx.doi.org/10.1101/032250

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Contact

Ahmed, Sanaa Afroz

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ACKNOWLEDGEMENTS

This project is funded by U.S. Defense Threat Reduction Agency [R-00059-12-0 and R-00332-13-0 to P.S.G.C.].

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Copyright

Los Alamos National Security, LLC (LANS) owns the copyright to PhaME, which it identifies internally as LA-CC-xx-xxxx. The license is GPLv3. See LICENSE for the full text.