UPP – Ultra-large alignments using Phylogeny-aware Profiles

UPP

:: DESCRIPTION

UPP addresses the problem of alignment of very large datasets, potentially containing fragmentary data.

::DEVELOPER

Siavash Mirarab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • Python

:: DOWNLOAD

 UPP

:: MORE INFORMATION

Citation

Ultra-large alignments using phylogeny-aware profiles.
Nguyen NP, Mirarab S, Kumar K, Warnow T.
Genome Biol. 2015 Jun 16;16(1):124.

CoMap 1.5.2 – Map Substitutions on a Phylogeny and Detect Coevolution

CoMap 1.5.2

:: DESCRIPTION

CoMap performs two kinds of tasks:

(Weighted) Probabilistic substitution mapping – Compute all (weighted) number of substitutions occurring on each branch of a tree, for each site of an alignment.
Co-evolution analysis – Using the substitution mapping, look for significantly groups of sites departing the null hypothesis of independence. Two kind of analyzes are provided: a pairwise analysis, presented in Dutheil et al. (2005), and a clustering analysis in Dutheil and Galtier (2007). In both cases, a parametric bootstrap approach is used to evaluate the significance of groups. Simulation results are written to separate files, a statistics software like R is required to look for the significance.

::DEVELOPER

Dr Julien Y. Dutheil

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Bio++

:: DOWNLOAD

CoMap

:: MORE INFORMATION

Cite the following article if you use the pairwise method:

Dutheil J, Pupko T, Jean-Marie A, Galtier N.
A model-based approach for detecting coevolving positions in a molecule.
Mol Biol Evol. 2005 Sep;22(9):1919-28.

Cite the following article if you use the clustering method:

Dutheil J, Galtier N.
Detecting groups of co-evolving positions in a molecule: a clustering approach.
BMC Evol Biol. 2007 Nov 30;7(1):242

Cite the following article if you use the candidate approach method:

Dutheil JY, Jossinet F, Westhof E.
Base pairing constraints drive structural epistasis in ribosomal RNA sequences.
Mol Biol Evol. 2010 Aug;27(8):1868-76

chromEvol 2.0 – Analyze Changes in Chromosome-number along a Phylogeny

chromEvol 2.0

:: DESCRIPTION

 chromEvol is a program for analyzing changes in chromosome-number along a phylogeny and for the inference of polyploidy.

::DEVELOPER

Mayrose Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux

:: DOWNLOAD

   chromEvol

:: MORE INFORMATION

Citation

Mayrose I, Barker MS, Otto SP. 2010.
Probabilistic models of chromosome number evolution and the inference of polyploidy.
Systematic Biology. 59(2):132-144

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.

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.

UnderlyingApproach – Alignment-Free Phylogeny of Whole Genomes using Underlying Subwords

UnderlyingApproach

:: DESCRIPTION

The Underlying Approach (UA) builds a scoring function based on this set of patterns, called underlying. This set is by construction linear in the size of input, without overlaps, and can be efficiently constructed. Results show the validity of our method in the reconstruction of phylogenetic trees, where the Underlying Approach outperforms the current state of the art methods. Moreover, the accuracy of UA is achieved with a very small number of subwords, which in some cases carry meaningful biological information.

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 UnderlyingApproach

:: MORE INFORMATION

Citation

Algorithms Mol Biol. 2012 Dec 6;7(1):34. doi: 10.1186/1748-7188-7-34.
Alignment-free phylogeny of whole genomes using underlying subwords.
Comin M, Verzotto D.

barphlye – Bayesian Rearrangement Phylogeny in Yersinia

barphlye

:: DESCRIPTION

barphlye supplements the BADGER software to analyze patterns present in ancient genome arrangements.

::DEVELOPER

The Darling Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX
  • R

:: DOWNLOAD

barphlye

:: MORE INFORMATION

Citation

PLoS Genet, 4 (7), e1000128 2008 Jul 18
Dynamics of Genome Rearrangement in Bacterial Populations
Aaron E Darling , István Miklós, Mark A Ragan

RaPPer – Generate Random perfect Phylogeny Matrix

RaPPer

:: DESCRIPTION

RaPPer will generate random perfect phylogeny matrix with following conditions.

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • MatLab

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Adv Appl Bioinform Chem. 2010;3:89-96. doi: 10.2147/AABC.S13397. Epub 2010 Nov 16.
Construction of random perfect phylogeny matrix.
Sadeghi M1, Pezeshk H, Eslahchi C, Ahmadian S, Abadi SM.

PASSML / Passml_TM – Analysis of Phylogeny / Transmembrane Domain searching from Aligned Amino Acid Sequences

PASSML / Passml_TM

:: DESCRIPTION

PASSML (‘Phylogeny and Secondary Structure using Maximum Likelihood’) has been developed to implement an evolutionary model that combines protein secondary structure and amino acid replacement.

Passml_TM implement an evolutionary model that permits analysis of phylogeny and transmembrane domain searching from aligned amino acid sequences.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 PASSML / Passml_TM

:: MORE INFORMATION

Citation

Bioinformatics. 1998;14(8):726-33.
PASSML: combining evolutionary inference and protein secondary structure prediction.
Liò P, Goldman N, Thorne JL, Jones3 DT.