:: DESCRIPTION
GO4genome is a prokaryotic phylogeny based on genome organization.
::DEVELOPER
Computational Protein Design and Evolution at the University of Regensburg
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Mol Evol. 2009 May;68(5):550-62. doi: 10.1007/s00239-009-9233-6.
GO4genome: a prokaryotic phylogeny based on genome organization.
Merkl R, Wiezer A.
:: DESCRIPTION
MaxTiC (Maximum Time Consistency) is a software which takes as input a species tree and a series of (possibly inconsistent) time constraints between its internal nodes, weighted by confidence scores.
::DEVELOPER
Computational Methods for Paleogenomics and Comparative Genomics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
:: DESCRIPTION
Prunetree is a program for trimming taxa off phylogenies. You can make subtrees by either including (or excluding) a specific group of taxa. In addition, it also has options to arbitrarily transform internode branch lengths (BL) following a speciational model (all BL = 1) or following Pagel?s method (all taxa aligned and all internode BL = 1).
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
ProGraphMSA is a state-of-the-art multiple sequence alignment tool which produces phylogenetically sensible gap patterns while maintaining robustness by allowing alternative splicings and errors in the branching pattern of the guide tree.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citaion
BMC Bioinformatics. 2012 Jun 13;13:129. doi: 10.1186/1471-2105-13-129.
Fast and robust multiple sequence alignment with phylogeny-aware gap placement.
Szalkowski AM.
:: DESCRIPTION
SVAMP is standalone desktop application to visualise variants (SNPs and indels) and peform realtime analysis on selected regions of a genome on specific samples. SVAMP has some interesting features like phylogeography,allele frequency map and principal coordinate analysis.
::DEVELOPER
Computational Bioscience Research Center, King Abdullah University of Science and Technology
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Apr 23. [Epub ahead of print]
SVAMP: sequence variation analysis, maps and phylogeny.
Naeem R1, Hidayah L, Preston MD, Clark TG, Pain A.
:: DESCRIPTION
Geptop is a webserver, which first provides a platform to detect essential gene sets over bacterial species, by comparing orthology and phylogeny of query protein sets with essential gene datasets determined experimentally (from DEG database).
::DEVELOPER
Microbe and Drug Bioinformatics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wen QF, Wei W, Guo FB.
Geptop 2.0: Accurately Select Essential Genes from the List of Protein-Coding Genes in Prokaryotic Genomes.
Methods Mol Biol. 2022;2377:423-430. doi: 10.1007/978-1-0716-1720-5_23. PMID: 34709630.
PLoS One. 2013 Aug 15;8(8):e72343. doi: 10.1371/journal.pone.0072343. eCollection 2013.
Geptop: a gene essentiality prediction tool for sequenced bacterial genomes based on orthology and phylogeny.
Wei W1, Ning LW, Ye YN, Guo FB.
:: DESCRIPTION
Ceiba is a program for visualization and navigation of large phylogenetic trees, and annotation of these trees with collections of images.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 May 9. [Epub ahead of print]
Ceiba: scalable visualization of phylogenies and 2D/3D image collections.
Sanderson MJ.
:: DESCRIPTION
BAMBE (Bayesian Analysis in Molecular Biology and Evolution) is a free software package for the Bayesian analysis of phylogenies. The package includes programs for analyzing aligned DNA or RNA sequence data and allows data sets with gaps or indeterminate sites. The main program uses a variety of Metropolis-Hastings algorithms to sample from the joint posterior distribution of phylogenetic trees and likelihood model parameters. Other programs in the distribution help in analysis of the sampled trees and parameter values.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Simon, D. and B. Larget. 2000.
Bayesian analysis in molecular biology and evolution (BAMBE), version 2.03 beta.
Department of Mathematics and Computer Science, Duquesne University.
:: DESCRIPTION
pHMM-Tree is the first software to generate a phylogeny of profile hidden markov models (HMMs).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Huo L, Zhang H, Huo X, Yang Y, Li X, Yin Y.
pHMM-tree: phylogeny of profile hidden Markov models.
Bioinformatics. 2017 Apr 1;33(7):1093-1095. doi: 10.1093/bioinformatics/btw779. PMID: 28062446; PMCID: PMC5860389.
:: DESCRIPTION
PUmPER is a framework to build automated pipelines that can perpetually update phylogenetic trees. PUmPER makes use of PHLAWD and RAxML-Light or ExaML to perpetually update Genbank datasets and simultaneously update inferred phylogenetic trees.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PUmPER: phylogenies updated perpetually.
Izquierdo-Carrasco F, Cazes J, Smith SA, Stamatakis A.
Bioinformatics. 2014 May 15;30(10):1476-7. doi: 10.1093/bioinformatics/btu053.
