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

fastHN – Fast Tool for Minimum Hybridization Networks

fastHN

:: DESCRIPTION

fastHN is a program for computing the hybridization number , a maximum acyclic agreement forest (MAAF) , or all maximum acyclic agreement forests (MAAFs) of two given phylogenetic trees. Once our programs find an MAAF, they also construct an optimal hybridization network .

::DEVELOPER

Chen Lab  & Lusheng Wang 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 fastHN

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Jul 2;13:155.
A fast tool for minimum hybridization networks.
Chen ZZ, Wang L, Yamanaka S.

mtree – Reticulate Networks of Multiple Phylogenetic Trees

mtree

:: DESCRIPTION

mtree is a set of softwares for constructing Hyplogenetic Networks from Multiple Phylogenetic Trees.

CMPT (Programs for Computing MAAF, MAAFs, MAF, MAFs of Multiple Phylogenetic Trees) are Programs for computing a maximum agreement forest (MAF) , all maximum agreement forests (MAFs) , a maximum acyclic agreement forest (MAAF) , or all maximum acyclic agreement forests (MAAFs) of two or more given phylogenetic trees. Once our programs find an MAAF, they also construct a reticulate network with the minimum number of reticulation vertices.

MaafB are programs for estimating lower bounds on the reticulation numbers of reticulate networks for multiple phylogenetic trees.

::DEVELOPER

Chen Lab  & Lusheng Wang 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /Linux/MacOsX

:: DOWNLOAD

 mtree

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2012 Mar-Apr;9(2):372-84. doi: 10.1109/TCBB.2011.137
Algorithms for Reticulate Networks of Multiple Phylogenetic Trees.
Chen ZZ, Wang L.

HybridNet – Compute rSPR Distances, Hybridization Numbers, and Hybridization Networks

HybridNet

:: DESCRIPTION

 HybridNet is a programs for computing the rSPR distance , a maximum agreement forest (MAF) , all maximum agreement forests (MAFs) , the hybridization number , a maximum acyclic agreement forest (MAAF) , or all maximum acyclic agreement forests (MAAFs) of two given phylogenetic trees. Once our programs find an MAAF, they also construct an optimal hybridization network .

::DEVELOPER

Chen Lab  & Lusheng Wang 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 HybridNet

:: MORE INFORMATION

Citation

HybridNET: a tool for constructing hybridization networks.
Chen ZZ, Wang L.
Bioinformatics. 2010 Nov 15;26(22):2912-3. doi: 10.1093/bioinformatics/btq548.

SPACoDi 0.1 / spacodiR 0.13.0115 – Structuring of Phylogenetic Diversity

SPACoDi 0.1 / spacodiR 0.13.0115

:: DESCRIPTION

SPACoDi (Spatial & Phylogenetic Analysis of Community Diversity) is primarily designed to characterise the structure of communities using inventory data in the form of a presence/absence or abundance species-plot matrix. The structure can be interpreted according to the spatial position of plots (subcommunities) and/or according to the phylogenetic or functional relationships between species (community phylogenetic structure)

spacodiR is a R package of SPACoDi.

::DEVELOPER

Olivier Hardy @ Evolutionary Biology & Ecology, Université Libre de Bruxelles

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SPACoDi  , spacodiR

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Sep 1;27(17):2437-8. Epub 2011 Jul 6.
spacodiR: structuring of phylogenetic diversity in ecological communities.
Eastman JM, Paine CE, Hardy OJ.

phylotools 0.2.2 – Phylogenetic Tools for Ecologists

phylotools 0.2.2

:: DESCRIPTION

phylotools is a software of building supermatrix for DNA barcodes using different genes, calculating the inequality among lineages and phylogenetic similarity for very large dataset using slicing methods by invoking Phylocom.

::DEVELOPER

Jinlong Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 phylotools

:: MORE INFORMATION

 

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