PHAST 1.3 / RPHAST 1.6 – Phylogenetic Analysis with Space/Time Models / for R

PHAST 1.3 / RPHAST 1.6

:: DESCRIPTION

PHAST is a freely available software package for comparative and evolutionary genomics. It consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations.

RPHAST: Phylogenetic Analysis with Space/Time Models… in R

::DEVELOPER

Siepel Lab, Pollard Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 PHAST / RPHAST 

 :: MORE INFORMATION

Citation

Brief Bioinform. 2011 Jan;12(1):41-51. doi: 10.1093/bib/bbq072. Epub 2010 Dec 21.
PHAST and RPHAST: phylogenetic analysis with space/time models.
Hubisz MJ1, Pollard KS, Siepel A.

MUTPATH – Map Mutational Paths through Protein Sequence Space

MUTPATH

:: DESCRIPTION

mutpath is a Python package for identifying mutational paths through sequence space generated using the MarkovJumps feature of BEAST.

::DEVELOPER

Bloom Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 mutpath

:: MORE INFORMATION

Citation

L. Ian Gong and Jesse D. Bloom.
Epistatically interacting substitutions are enriched during adaptive protein evolution.”
PLoS Genetics. 10:e1004328 (2014)

PSpacE Beta – Protein Structure Space Explorer

PSpacE

:: DESCRIPTION

The PSpacE is an open-source, platform-independent web application for direct exploration of protein structure space in 3D.

::DEVELOPER

Biocomputing and Media Research Lab

:: SCREENSHOTS

PSpacE

:: REQUIREMENTS

  • WEb Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 14:S10. doi: 10.1186/1471-2105-14-S14-S10. Epub 2013 Oct 9.
Towards human-computer synergetic analysis of large-scale biological data.
Singh R, Yang H, Dalziel B, Asarnow D, Murad W, Foote D, Gormley M, Stillman J, Fisher S.

RNAHeliCes 2.0.14 – RNA Folding Space Analysis

RNAHeliCes 2.0.14

:: DESCRIPTION

RNAHeliCes is a tool for RNA folding space analysis. It abstracts from structural detail and maps structures using a position-specific abstraction based on helices.

::DEVELOPER

Cyanolab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 RNAHeliCes

:: MORE INFORMATION

Citation:

RNA. 2012 Dec;18(12):2135-47. doi: 10.1261/rna.033548.112. Epub 2012 Oct 25.
Abstract folding space analysis based on helices.
Huang J1, Backofen R, Voß B.

SPACE – Tools for Structure Prediction and Analysis based on Complementarity with Environment

SPACE

:: DESCRIPTION

SPACE is a suite of SPACE tools for analysis and prediction of structures of biomolecules and their complexes.

::DEVELOPER

Edelman-Sobolev Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SPACE

:: MORE INFORMATION

Citation:

SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment.
Sobolev V, Eyal E, Gerzon S, Potapov V, Babor M, Prilusky J, Edelman M.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W39-43.

Bis-SNP 0.82.2 – Bisulfite Space Genotyper & Methylation Caller

BisSNP 0.82.2

:: DESCRIPTION

BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and accurate DNA methylation calling in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq, RRBS and any other bisulfite treated sequencing) with Illumina directional library protocol.

::DEVELOPER

USC Epigenome Center

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • java
  • perl 

:: DOWNLOAD

 Bis-SNP

:: MORE INFORMATION

Citation

Genome Biol. 2012 Jul 11;13(7):R61. [Epub ahead of print]
Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data.
Liu Y, Siegmund KD, Laird PW, Berman BP.