P4P – Peptidomes for Phylogenies

P4P

:: DESCRIPTION

P4P is a bioinformatics web service which has been conceived for bacterial strain classification based on peptide datasets. These peptide datasets are obtained from proteins by the in silico action of the three main human gut endoproteases (pepsin, trypsin and chemotrypsin). Peptides can be filtered by isolectric point, subcellular location, or amino acid length.

::DEVELOPER

SING Group.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Blanco-Míguez A, Fdez-Riverola F, Lourenço A, Sánchez B.
P4P: a peptidome-based strain-level genome comparison web tool.
Nucleic Acids Res. 2017 Jul 3;45(W1):W265-W269. doi: 10.1093/nar/gkx389. PMID: 28482090; PMCID: PMC5570244.

DupLoCut – Duplication Loss Phylogeny by Cutting Planes

DupLoCut

:: DESCRIPTION

DupLoCut computes ancestral gene orders, given a phylogenetic tree and gene orders assigned to the leaves of the tree. It attempts to find the most parsimony assignment of gene orders under the duplication-loss evolutionary model.

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX

:: DOWNLOAD

DupLoCut

:: MORE INFORMATION

Citation

J Comput Biol. 2013 Sep;20(9):643-59. doi: 10.1089/cmb.2013.0057.
The duplication-loss small phylogeny problem: from cherries to trees.
Andreotti S1, Reinert K, Canzar S.

SPRUCE – Somatic Phylogeny Reconstruction using Combinatorial Enumeration

SPRUCE

:: DESCRIPTION

SPRUCE is an algorithm that infers a multi-state perfect phylogeny describing the evolutionary history of the somatic mutations (SNVs and CNVs) of a tumor given multi-sample bulk sequencing data. Specifically, the input to SPRUCE are variant allele frequencies and copy-number mixing proportions for each SNV in each sample.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++

:: DOWNLOAD

SPRUCE

:: MORE INFORMATION

Citation:

El-Kebir M, Satas G, Oesper L, Raphael BJ.
Inferring the Mutational History of a Tumor Using Multi-state Perfect Phylogeny Mixtures.
Cell Syst. 2016 Jul;3(1):43-53. doi: 10.1016/j.cels.2016.07.004. PMID: 27467246.

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