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.

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

CME Group

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ProtASR

:: MORE INFORMATION

Citation

Arenas M, Weber CC, Liberles DA, Bastolla U.
ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability.
Syst Biol. 2017 Nov 1;66(6):1054-1064. doi: 10.1093/sysbio/syw121. PMID: 28057858.

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.

Phylo-SMC r0 – Bayesian Phylogenetic Inference tool based on Sequential Monte Carlo

Phylo-SMC r0

:: DESCRIPTION

Phylo-SMC is a Bayesian phylogenetic inference tool based on Sequential Monte Carlo (SMC), an alternative to the standard Markov Chain Monte Carlo approach (MCMC).

::DEVELOPER

Alexandre BouchardSriram Sankararaman, and Michael I. Jordan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX / Windows
  • Java
  • Phylip
  • Mrbayes
  • R package

:: DOWNLOAD

 Phylo-SMC

:: MORE INFORMATION

Citation

Syst Biol. 2012 Jul;61(4):579-93. doi: 10.1093/sysbio/syr131.
Phylogenetic inference via sequential Monte Carlo.
Bouchard, A., Sankararaman, S., Jordan, M.I

TAGD – Phylogenetically Informative Substring Extraction

TAGD

:: DESCRIPTION

TAGD will generate tags for a specific branch of a tree, given the tree’s structure as well as the sequence for all its taxa.

::DEVELOPER

the Kim Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 TAGD

:: MORE INFORMATION

Citation

S. Angelov, B. Harb, S. Kannan, S. Khanna, and J. Kim. 2007.
Efficient Enumeration of Phylogenetically Informative Substrings.
Journal of Computational Biology., 14(6): 701-723.

LGTNet 1.0 – Fast inference of lateral Genetic Transfer Networks

LGTNet 1.0

:: DESCRIPTION

LGTNet is a software to infer networks of lateral genetic transfer (LGT) from sequence data. In contrast to traditional techniques based on multiple sequence alignments and phylogenetic trees LGTNet is an alignment- and tree-free method.

::DEVELOPER

LGTNet team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 LGTNet

:: MORE INFORMATION

Citation

S. Maetschke, L. McIntyre, C. Chan, M. Ragan
Fast inference of lateral genetic transfer networks.

LcaMap – Simultaneous Identification of Duplications, Losses and Lateral Gene Transfers

LcaMap

:: DESCRIPTION

LcaMap is a software for simultaneous identification of duplication, losses and lateral gene transfers. LcaMap takes a gene tree G, a species tree S, and the costs of a lateral gene transfer, a gene duplication, and a gene loss as its input. It outputs all minimum-cost LCA-reconciliations between G and S.

::DEVELOPER

Lusheng Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 LcaMap

:: MORE INFORMATION

Exit mobile version