:: DESCRIPTION
SNV-PPILP is a fast and easy to use tool for refining GATK’s Unified Genotyper SNV calls, for multiple samples assumed to form a phylogeny.
::DEVELOPER
GSA (Genome-scale algorithmics) group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
SNV-PPILP: Refined SNV calling for tumor data using perfect phylogenies and ILP.
van Rens KE, Mäkinen V, Tomescu AI.
Bioinformatics. 2014 Nov 13. pii: btu755
:: DESCRIPTION
BPhyOG is an interactive web server for reconstruction of whole-genome bacterial phylogenies based on overlapping genes, and also allows users to browse overlapping genes to acquire more information about subtree-specific genomes or all the 177 genomes.
:: DEVELOPER
Laboratory of Computational Molecular Biology, Beijing Normal University.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
BPhyOG: an interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes.
Luo Y, Fu C, Zhang DY, Lin K.
BMC Bioinformatics. 2007 Jul 25;8:266.
:: DESCRIPTION
Conserve IV is an application for calculating diversity in site-based conservation and assessing preservation schemes. Specifically, it calculates diversity metrics over a phylogeny or series of phylogenies. Individual taxa can be included or excluded from calculations, simulating the state of their preservation and possible accompanying loss of evolutionary history. Taxa can be grouped into sets manually or via several automatic methods, and these sets activated or inactivated as one. Where multiple phylogenies are provided, confidence limits are calculated for diversity metrics. Finally, capability is provided for summing external costs, expenditure that is specific to preserving individual taxa.
::DEVELOPER
Paul-Michael Agapow and Austin Burt (a.burt@imperial.ac.uk), Dept. Biology, University College London
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
LICHeE (Lineage Inference for Cancer Heterogeneity and Evolution) is a novel method that automates the phylogenetic inference of cancer progression from multiple somatic samples.
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Fast and scalable inference of multi-sample cancer lineages.
Popic V, Salari R, Hajirasouliha I, Kashef-Haghighi D, West RB, Batzoglou S.
Genome Biol. 2015 May 6;16(1):91
:: DESCRIPTION
RASP is a tool for inferring ancestral state using S-DIVA (Statistical dispersal-vicariance analysis), Lagrange (DEC), Bayes-Lagrange (S-DEC), BayArea, BBM (Bayesian Binary MCMC), BayesTraits and ChromEvol.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
S-DIVA (Statistical Dispersal-Vicariance Analysis): A tool for inferring biogeographic histories.
Yu Y, Harris AJ, He X.
Mol Phylogenet Evol. 2010 Aug;56(2):848-50. doi: 10.1016/j.ympev.2010.04.011
RASP (Reconstruct Ancestral State in Phylogenies): A tool for historical biogeography.
Yu Y, Harris AJ, Blair C, He X.
Mol Phylogenet Evol. 2015 Mar 26;87:46-49. doi: 10.1016/j.ympev.2015.03.008.
:: DESCRIPTION
PhyloPars provides an efficient and statistically consistent method of combining any number of empirical observations with the phylogenetic tree to arrive at complete set of estimates for missing parameter values.
::DEVELOPER
The Centre for Integrative Bioinformatics VU
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W179-84. doi: 10.1093/nar/gkp370.
PhyloPars: estimation of missing parameter values using phylogeny.
Bruggeman J1, Heringa J, Brandt BW.
:: DESCRIPTION
Picante is a software package that provides a comprehensive set of tools for analyzing the phylogenetic and trait diversity of ecological communities.
::DEVELOPER
Steven W. Kembel <steve.kembel at gmail.com>
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2010 Jun 1;26(11):1463-4. doi: 10.1093/bioinformatics/btq166. Epub 2010 Apr 15.
Picante: R tools for integrating phylogenies and ecology.
Kembel SW1, Cowan PD, Helmus MR, Cornwell WK, Morlon H, Ackerly DD, Blomberg SP, Webb CO.
:: DESCRIPTION
PhyloTrack is a JavaScript–based software tool that integrates the D3.js library for data visualization with the JBrowse tool for genome browser representation.
::DEVELOPER
:: SCREENSHOTS
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis.
Benavente ED, Coll F, Furnham N, McNerney R, Glynn JR, Campino S, Pain A, Mohareb FR, Clark TG.
BMC Bioinformatics. 2015 May 13;16:155. doi: 10.1186/s12859-015-0603-3.
:: DESCRIPTION
PICS-Ord (Pairwise Identity and Cost Scores Ordination) is a method to extract phylogeny information from hard-to-align regions of multiple sequence alignments.
::DEVELOPER
The Cartwright Lab @ ASU
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2011 Jan 7;12:10. doi: 10.1186/1471-2105-12-10.
PICS-Ord: unlimited coding of ambiguous regions by pairwise identity and cost scores ordination.
Lücking R, Hodkinson BP, Stamatakis A, Cartwright RA.
:: DESCRIPTION
PhISCS is a tool for sub-perfect tumor phylogeny reconstruction via integrative use of single cell and bulk sequencing data.
::DEVELOPER
Lab for Bioinformatics and Computational Genomics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Malikic S, Mehrabadi FR, Ciccolella S, Rahman MK, Ricketts C, Haghshenas E, Seidman D, Hach F, Hajirasouliha I, Sahinalp SC.
PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data.
Genome Res. 2019 Nov;29(11):1860-1877. doi: 10.1101/gr.234435.118. Epub 2019 Oct 18. PMID: 31628256; PMCID: PMC6836735.