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Fastphylo: Fast tools for phylogenetics

Mehmood Khan, Isaac Elias, Erik Sjölund, Kristina Nylander, Roman Guimera, Richard Schobesberger, Peter Schmitzberger, Jens Lagergren, Lars Arvestad
2013 BMC Bioinformatics  
Conclusions: Fastphylo is a fast, memory efficient, and easy to use software suite. Due to its modular architecture, fastphylo is a flexible tool for many phylogenetic studies.  ...  Results: We present fastphylo, a software package containing implementations of efficient algorithms for two common problems in phylogenetics: estimating DNA/protein sequence distances and reconstructing  ...  The computations were performed using the resources provided by SNIC through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) under Project b2012160: FastPhylo.  ... 
doi:10.1186/1471-2105-14-334 pmid:24255987 pmcid:PMC4225504 fatcat:47xbjep3anbm3nrnusse2quasm

The Eurasian invasion: phylogenomic data reveal multiple Southeast Asian origins for Indian Dragon Lizards

Jesse L. Grismer, James A. Schulte, Alana Alexander, Philipp Wagner, Scott L. Travers, Matt D. Buehler, Luke J. Welton, Rafe M. Brown
2016 BMC Evolutionary Biology  
Results: Results from our phylogenetic and biogeographic analyses revealed support for two independent colonizations of India from Eurasian ancestors during the early to late Eocene prior to the subcontinent's  ...  Many phylogenetic studies have demonstrated the Indian subcontinent brought with it an array of endemic faunas that evolved in situ during its journey, suggesting this isolated subcontinent served as a  ...  For field assistance we thank Indraneli Das and for assistance with UCE pipeline we thank Carl H. Oliveros.  ... 
doi:10.1186/s12862-016-0611-6 pmid:26896057 pmcid:PMC4759850 fatcat:d3vivgxdrjc2bc24kwyf2s7os4

Efficient Gene Tree Correction Guided by Genome Evolution

Emmanuel Noutahi, Magali Semeria, Manuel Lafond, Jonathan Seguin, Bastien Boussau, Laurent Guéguen, Nadia El-Mabrouk, Eric Tannier, Marc Robinson-Rechavi
2016 PLoS ONE  
Information for their full resolution may lie in the dependency between gene families and their genomic context.  ...  Compute D(g, g 0 ) for all g 0 2 E using Eq (2) End For End If Else If m(s)<V [s] Do {Perform V [s] − m(s) losses} Add V [s] − m A Multi-functional algorithm: ProfileNJ is a phylogenetic tool that generalizes  ...  It has been designed to be easily extensible to other tools. For example instead of asking the user to input his own orthology relations, tools for inferring putative orthologs can be included.  ... 
doi:10.1371/journal.pone.0159559 pmid:27513924 pmcid:PMC4981423 fatcat:otdbekpe7ve2veau5jhhqtarsy