:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: REQUIREMENTS
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
mutpath is a Python package for identifying mutational paths through sequence space generated using the MarkovJumps feature of BEAST.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
L. Ian Gong and Jesse D. Bloom.
“Epistatically interacting substitutions are enriched during adaptive protein evolution.”
PLoS Genetics. 10:e1004328 (2014)
:: 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
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
