Category: Phylogenetic Analysis

ProtASR 2.2 – Ancestral Sequence Reconstruction of Proteins accounting for Structural Constraints

ProtASR 2.2

:: DESCRIPTION

ProtASR is an evolutionary framework to reconstruct ancestral protein sequences accounting for structural constraints.

::DEVELOPER

Dr. Miguel Arenas

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ProtASR

:: MORE INFORMATION

Citation

Arenas M, Bastolla U.
ProtASR2: Ancestral reconstruction of protein sequences accounting for folding stability.
Methods Ecol Evol. 2020; 11: 248–257. https://doi.org/10.1111/2041-210X.13341

Network 10.2.0.0 – Phylogenetic Network Software

Network 10.2.0.0

:: DESCRIPTION

Network is used to reconstruct phylogenetic networks and trees, infer ancestral types and potential types, evolutionary branchings and variants, and to estimate datings. Network generates evolutionary trees and networks from genetic, linguistic, and other data. Network can then provide age estimates for any ancestor in the tree.

::DEVELOPER

Fluxus Technology Ltd

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Network

:: MORE INFORMATION

ProtEvol 1.0 – Maximum Likelihood Phylogenetic Inference with Selection on Protein Folding Stability

ProtEvol 1.0

:: DESCRIPTION

The program ProtEvol performs two kinds of computation.

  1. It computes the mean-field site-specific amino acid distributions that have minimal differences with respect to the background distribution and that constraint the average stability of the native state of the protein against both unfolding and misfolding. The program also computes an exchangeability matrix derived from an empirical substitution model or from a mutation model that can be used together with the site-specific distributions for applications in phylogenetic inference.
  2. It simulates protein evolution subject to the constraint of selection on the folding stability of the native state of the protein against both unfolding and misfolding.

::DEVELOPER

Unidad de Bioinformatica CBMSO

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  ProtEvol

:: MORE INFORMATION

Citation

Maximum likelihood phylogenetic inference with selection on protein folding stability.
Arenas M, Sánchez-Cobos A, Bastolla U.
Mol Biol Evol. 2015 Apr 2. pii: msv085.

SeaView 5.0.5 – Sequence Alignment and Phylogenetic Tree Building

SeaView 5.0.5

:: DESCRIPTION

SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.

::DEVELOPER

PRABI-Doua

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux

:: DOWNLOAD

 SeaView

:: MORE INFORMATION

Citation

Gouy M., Guindon S. & Gascuel O. (2010)
SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building.
Molecular Biology and Evolution 27(2):221-224.

SplitsTree 6.1.10 – Compute Phylogenetic Networks

SplitsTree 6.1.10

:: DESCRIPTION

SplitsTree uses the split decomposition method to analyse and visualize distance data, e.g. data derived from biosequences. SplitsTree4 is the leading application for computing unrooted phylogenetic networks from molecular sequence data. Given an alignment of sequences, a distance matrix or a set of trees, the program will compute a phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks.

::DEVELOPER

the Algorithms in Bioinformatics lab.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX

:: DOWNLOAD

SplitsTree

:: MORE INFORMATION

Citation

D. H. Huson and D. Bryant,
Application of Phylogenetic Networks in Evolutionary Studies
Mol. Biol. Evol., 23(2):254-267, 2006.

NimbleTree 2.6 – Make Phylogenetic Trees from Sequence Data

NimbleTree 2.6

:: DESCRIPTION

NimbleTree is a relatively user-friendly Windows program for making phylogenetic trees starting from sequence data.

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

NimbleTree

:: MORE INFORMATION

Before you download software you need to read disclaimer.

iBPP v2.1.3 – Bayesian Species Delimitation Integrating Genes and Traits data

iBPP v2.1.3

:: DESCRIPTION

iBPP is a program of integration of genes and traits for Bayesian Phylogenetics and Phylogeography.

::DEVELOPER

Solis-Lemus lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

iBPP

:: MORE INFORMATION

Citation

Solís-Lemus C, Knowles LL, Ané C.
Bayesian species delimitation combining multiple genes and traits in a unified framework.
Evolution. 2015 Feb;69(2):492-507. doi: 10.1111/evo.12582. Epub 2015 Jan 16. PMID: 25495061.

PhyloNetworks v0.14.2 – Analysis for Phylogenetic Networks

PhyloNetworks v0.14.2

:: DESCRIPTION

PhyloNetworks is a Julia package for the inference, manipulation, visualization, and use of phylogenetic networks in an interactive environment.

::DEVELOPER

Solis-Lemus lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOs
  • Julia

:: DOWNLOAD

PhyloNetworks

:: MORE INFORMATION

Citation

Solís-Lemus C, Bastide P, Ané C.
PhyloNetworks: A Package for Phylogenetic Networks.
Mol Biol Evol. 2017 Dec 1;34(12):3292-3298. doi: 10.1093/molbev/msx235. PMID: 28961984.

GO4genome – Whole Genome Phylogeny

GO4genome

:: 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

  • Linux
  • C COmpiler

:: DOWNLOAD

 GO4genome

:: 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.