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• File:Phylogenetic Analyses video.png (1,439 × 806 (249 KB)) - 18:31, 4 March 2014

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• Talk:BioC Requirements Information Gathering
  ...t run over a month. Between checkpointing and better software, most of the analyses that I've seen running over 30days on our lab cluster or Fisher were
  3 KB (493 words) - 21:42, 2 November 2011
• Viralmsa
  ...genetic inference, as insertions with respect to the reference likely lack phylogenetic information), but it may not be appropriate for all contexts.
  3 KB (357 words) - 19:56, 27 May 2022
• PHYling
  The aligned markers can be extracted from protein sequences for phylogenetic analyses and also projected into coding sequence alignments for codon-based
  3 KB (375 words) - 18:17, 3 June 2022
• BMGE
  ...e-block-mapping-and-gathering-with-entropy-a-new-software-for-selection-of-phylogenetic-informative-regions-from-multiple-sequence-alignments/}} ...ered as not suited for phylogenetic inference and then removed. Simulation analyses show that the character trimming performed by BMGE produces datasets leadin
  3 KB (407 words) - 13:04, 15 August 2022
• PhaME
  ...sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (genes under positive selection) using CDS SNPs.
  2 KB (287 words) - 14:18, 9 March 2020
• PhyML
  ...r of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but g
  3 KB (465 words) - 20:22, 12 August 2022
• SWSC-EN
  ...please see the accompanying paper, and the repository for replicating the analyses in that paper.
  3 KB (328 words) - 14:46, 8 January 2020
• Ksnp
  phylogenetic analysis of genomes without genome alignment or reference genomes. Gardner, S.N. and Slezak, T.R. 2010. Scalable SNP analyses of 100+ bacterial or
  3 KB (327 words) - 12:56, 15 August 2022
• ExaBayes
  ExaBayes is a tool for Bayesian phylogenetic analyses. It implements a Markov chain Monte Carlo sampling approach that allows to ...u, Marc a Suchard, and John P Huelsenbeck. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic biology,
  7 KB (886 words) - 21:12, 21 December 2022
• PAML
  PAML is a package of programs for phylogenetic analyses of DNA or protein
  3 KB (367 words) - 20:12, 12 August 2022
• Mvftools
  ...coding allows for rapid computation of phylogenetic and population genetic analyses, and small file sizes that enable data sharing and distribution.
  3 KB (370 words) - 13:58, 30 April 2020
• Clann
  ...J.O. 2005 Clann: investigating phylogenetic information through supertree analyses. Bioinformatics 21(3): 390-2.
  3 KB (438 words) - 18:30, 12 August 2022
• QIIME2
  ...al analyses such as OTU picking, taxonomic assignment, and construction of phylogenetic trees from representative sequences of OTUs, and through downstream statist
  3 KB (435 words) - 15:15, 19 August 2022
• RAxML
  ...am for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It was originally derived from fastDNAml which in turn was derived f ...essors to use. In our testing, values over 8 do not significantly speed up analyses and should be avoided. It is important to use the '''-T''' flag which tells
  7 KB (1,050 words) - 21:31, 21 August 2022
• QIIME
  ...al analyses such as OTU picking, taxonomic assignment, and construction of phylogenetic trees from representative sequences of OTUs, and through downstream statist
  4 KB (555 words) - 15:15, 19 August 2022