lizhizhong1992 / phylogenomics_pipeline

After gene family clusing using Orthofinder, single copy nuclear genes and low copies nuclear genes were used to infer the phlogenies between related taxon, three types of data or algorithms were implemented to achive this goal. the perl script phylogenomics_4dtv.pl inferred the phylogeny using four-fold degenerated sites (4DTvs) of combined single copy nuclear genes;

phylogenomics_pipeline

Phylogeny inference based on genome-wide data is a routine step for newly sequenced genomes.After gene family clustering implemented in Orthofinder or OrthoMCL, we can reconstruct the phlogeny using both single copy nuclear genes or low-copy nuclear genes. We found that the available species tree derived from built-in program STAG of Orthofinder was not accurate among closely related species, ie,taxon within a family. three independent perl scripts a. phylogenomics_4dtv.pl. phylogeny inference using four-fold degenerated sites of concatenate loci. b. phylogenomics_astral.pl phylogeny inference using raxml gene tree,and summary methods colaescent methods implented in ASTRAL-II based single copy nuclear gene. c. phylogenomics_para.pl. phylogeny inference using low copy nuclear genes implemented in ASTRAL-Pro (Zhang et al 2019), scripts or software used in this pipleline cited as:

Alexandros Stamatakis, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1312–1313, https://doi.org/10.1093/bioinformatics/btu033

Chao Zhang, Celine Scornavacca, Erin K. Molloy, Siavash Mirarab bioRxiv 2019.12.12.874727; doi:https://doi.org/10.1101/2019.12.12.874727Biology and Evolution, Volume 30, Issue 4, April 2013, Pages 772–780, https://doi.org/10.1093/molbev/mst010

Kazutaka Katoh, Daron M. Standley, MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability, Molecular ASTRAL-Pro: quartet-based species tree inference despite paralogy

Mikita Suyama, David Torrents, and Peer Bork (2006) PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.Nucleic Acids Res. 34, W609-W612.

Mikita Suyama, David Torrents, Peer Bork, PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments, Nucleic Acids Research, Volume 34, Issue suppl_2, 1 July 2006, Pages W609–W612, https://doi.org/10.1093/nar/gkl315

Salvador Capella-Gutiérrez, José M. Silla-Martínez, Toni Gabaldón, trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, Volume 25, Issue 15, 1 August 2009, Pages 1972–1973, https://doi.org/10.1093/bioinformatics/btp348

Siavash Mirarab, Tandy Warnow, ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes, Bioinformatics, Volume 31, Issue 12, 15 June 2015, Pages i44–i52, https://doi.org/10.1093/bioinformatics/btv234

Stajich JE, Block D, Boulez K, et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002;12(10):1611-1618. doi:10.1101/gr.361602

Installation:

1. the pipeline phylogenomics_4dtvs.pl need BioPerl 1a. >perl -MCPAN -e shell cpan>install Bundle::CPAN cpan>q

1b. upgrade cpan >cpan cpan>install Module::Build cpan>o conf prefer_installer MB cpan>o conf commit cpan>q

1c. install two modules cpan>install Bio::SeqIO cpan>install Bio::AlignIO cpan>install Bio::AlignI other binary scripts were ready for use.

the orhogroups_list can be obtained used the perl script summary.pl