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:
- 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