Cocos – Reconstructing Phylogenies of Multi-Domain Proteins

Cocos

:: DESCRIPTION

Cocos is a tool to construct phylogenies of multi-domain proteins.

::DEVELOPER

Research Group Microbial Virulence

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

 Cocos

:: MORE INFORMATION

Citation

Cocos: Constructing multi-domain protein phylogenies.
Homilius M, Wiedenhoeft J, Thieme S, Standfuß C, Kel I, Krause R.
PLoS Curr. 2011 Jun 9;3:RRN1240. doi: 10.1371/currents.RRN1240.

BitPhylogeny 0.99 – Reconstruct Intra-tumor Evolutionary Pathways

BitPhylogeny 0.99

:: DESCRIPTION

BitPhylogeny is a probabilistic framework to reconstruct intra-tumor evolutionary pathways.

::DEVELOPER

the Markowetz lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python
  • R

:: DOWNLOAD

 BitPhylogeny

:: MORE INFORMATION

Citation

Genome Biol. 2015 Feb 13;16:36. doi: 10.1186/s13059-015-0592-6.
BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies.
Yuan K, Sakoparnig T, Markowetz F, Beerenwinkel N.

MEDICC – Minimum Event Distance for Intra-tumour Copy number Comparisons

MEDICC

:: DESCRIPTION

MEDICC harnesses the power of a finite-state automaton representation of genomic profiles to model genomic rearrangement events with horizontal dependencies.

::DEVELOPER

the Markowetz lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

 MEDICC

:: MORE INFORMATION

Citation

Phylogenetic quantification of intra-tumour heterogeneity.
Schwarz RF, Trinh A, Sipos B, Brenton JD, Goldman N, Markowetz F.
PLoS Comput Biol. 2014 Apr 17;10(4):e1003535. doi: 10.1371/journal.pcbi.1003535

TreeSim 2.4 / TreeSimGM 2.3 – Simulating Trees under the Birth-Death Model / under a General Model

TreeSim 2.4 / TreeSimGM 2.3

:: DESCRIPTION

TreeSim is an R package for simulating phylogenetic trees.

TreeSimGM: Simulating Phylogenetic Trees under a General Model

::DEVELOPER

Computational Evolution group at ETH

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • R package

:: DOWNLOAD

  TreeSim , TreeSimGM

:: MORE INFORMATION

Citation

Syst Biol. 2011 Oct;60(5):676-84. doi: 10.1093/sysbio/syr029. Epub 2011 Apr 11.
Simulating trees with a fixed number of extant species.
Stadler T.

TreePar 3.3 – Estimating Birth and Death Rates based on Phylogenies

TreePar 3.3

:: DESCRIPTION

TreePar is an R package for inferring speciation and extinction rates based on phylogenetic trees.

::DEVELOPER

Computational Evolution group at ETH

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • R package

:: DOWNLOAD

 TreePar

:: MORE INFORMATION

Citation

Stadler, T,
Mammalian phylogeny reveals recent diversification rate shifts,
Proc. Nat. Acad. Sci. (2011) 108:6187-6192.

PAL 1.5.1 – Java Library for Molecular Evolution & Phylogenetics

PAL 1.5.1

:: DESCRIPTION

PAL (Phylogenetic Analysis Library) project is a collaborative effort to provide a high quality Java library for use in molecular evolution and phylogenetics. Updates of PAL are released in regular intervals. At present (version 1.4) PAL consists of approximately 200 public classes/interfaces in 16 packages with a total of more than 35,000 lines of Java code.

::DEVELOPER

PAL Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

PAL

:: MORE INFORMATION

Citation

Drummond, A., and K. Strimmer. 2001.
PAL: An object-oriented programming library for molecular evolution and phylogenetics.
Bioinformatics 17: 662-663.

Vanilla 1.2 – Programs to Access Features in PAL

Vanilla 1.2

:: DESCRIPTION

Vanilla is a collection of command line programs written in Java to access some selected features in PAL, a Java library for molecular evolution and phylogenetics (see http://www.cebl.auckland.ac.nz/pal-project/ for details on PAL). Note that Vanilla does not provide all functionality available in PAL.

::DEVELOPER

Strimmer Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

Vanilla

:: MORE INFORMATION

Citation

Drummond, A., and K. Strimmer. 2001.
PAL: An object-oriented programming library for molecular evolution and phylogenetics.
Bioinformatics 17: 662-663.

BEGFE 1.1 – Bayesian Estimation of Gene Family Evolution

BEGFE 1.1

:: DESCRIPTION

BEGFE implements a Markov Chain Monte Carlo algorithm to estimate the posterior probability distribution of the birth and death rate parameters and the numbers of gene copies at the internodes of the phylogenetic tree. In addition, BEGFE can simulate gene family data under the birth and death model.

::DEVELOPER

Phylogenetics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/ Windows

:: DOWNLOAD

BEGFE

:: MORE INFORMATION

Citation

Liu, L., L. Yu, V. Kalavacharla, Z. Liu.
A Bayesian model for gene family evolution.
BMC Bioinformatics. 2011, 12:426

Phybase 2.0 – R package for Phylogenetic Analysis

Phybase 2.0

:: DESCRIPTION

PHYBASE provides functions to read, write, manipulate, simulate, estimate, and summarize phylogenetic trees (gene trees and species trees).

::DEVELOPER

Phylogenetics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/ Windows / Linux
  • R

:: DOWNLOAD

Phybase

:: MORE INFORMATION

Citation

Bioinformatics, 26 (7), 962-3 2010 Apr 1
Phybase: An R Package for Species Tree Analysis
Liang Liu 1, Lili Yu

MP-EST 2.0 – Estimating Species Trees from a set of Gene Trees

MP-EST 2.0

:: DESCRIPTION

MP-EST estimates species trees from a set of gene trees by maximizing a pseudo-likelihood function.

::DEVELOPER

Phylogenetics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/ Windows

:: DOWNLOAD

MP-EST

:: MORE INFORMATION

Citation

Liu, L., L. Yu, S.V. Edwards.
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model.
BMC Evol. Biol. 2010, 10:302.