:: DESCRIPTION
MargFreq is a relatively user-friendly Windows program that does a repetitive task – calculating the marginal frequencies at each position of a nucleotide/amino acid sequence. This program accepts sequence alignments in many different formats. It also does some rudimentary analysis for covariation.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Before you download software you need to read disclaimer.
:: DESCRIPTION
MetaCherchant is a tool for analyzing genomic context of antibiotic resistance genes in gut microbiota.
::DEVELOPER
Computer Technologies Laboratory, National Research University of Information Technologies,
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation
Olekhnovich EI, Vasilyev AT, Ulyantsev VI, Kostryukova ES, Tyakht AV.
MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota.
Bioinformatics. 2018 Feb 1;34(3):434-444. doi: 10.1093/bioinformatics/btx681. PMID: 29092015.
:: DESCRIPTION
Correlation Finder is a free software which allows to seek correlations between nucleotides in genomic sequences. It computes some parameters for each analyzed correlation: the relative abundance, the conditional probability, the frequency of the words making up the correlation.
::DEVELOPER
Gruppo di Biologia Computazionale
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
In Silico Biol. 2005;5(5-6):465-8.
Correlation Finder.
Piva F1, Principato G.
:: DESCRIPTION
CovaRNA / CovStat is a novel index-based computational method to detect long-range covariation on a genomic scale, as well as for determining the statistical significance of observed covariation patterns in alignment pairs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bindewald E, Shapiro BA.
Computational detection of abundant long-range nucleotide covariation in Drosophila genomes.
RNA. 2013 Sep;19(9):1171-82. doi: 10.1261/rna.037630.112. Epub 2013 Jul 25. PMID: 23887147; PMCID: PMC3753924.
:: DESCRIPTION
R3D Align is a web application for locally optimized, nucleotide to nucleotide pairwise alignments of RNA 3D structure
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.
Rahrig RR, Petrov AI, Leontis NB, Zirbel CL.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W15-21. doi: 10.1093/nar/gkt417.
:: DESCRIPTION
Gene Spaghetti is GPL software for visualizing base and amino acid usage in a genome.
::DEVELOPER
Victorian Bioinformatics Consortium
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
h5vc contains functions to interact with tally data from NGS experiments that is stored in HDF5 files.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 May 15;30(10):1464-6. doi: 10.1093/bioinformatics/btu026. Epub 2014 Jan 21.
h5vc: scalable nucleotide tallies with HDF5.
Pyl PT, Gehring J, Fischer B, Huber W.
:: DESCRIPTION
ntHash is a hashing algorithm tuned for processing DNA/RNA sequences. It performs the best when calculating hash values for adjacent k-mers in an input sequence, operating an order of magnitude faster than the nearest competitors in typical use cases.
::DEVELOPER
Canada’s Michael Smith Genome Sciences Centre
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
ntHash: recursive nucleotide hashing.
Mohamadi H, Chu J, Vandervalk BP, Birol I.
Bioinformatics. 2016 Jul 16. pii: btw397.
:: DESCRIPTION
BiasAway is an open-access tool for generating multiple different sequence backgrounds of comparable nucleotide composition relative to a set of input sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Worsley Hunt R, Mathelier A, Del Peso L, Wasserman WW.
Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment.
BMC Genomics. 2014 Jun 13;15(1):472. doi: 10.1186/1471-2164-15-472. PMID: 24927817; PMCID: PMC4082612.
A. Khan, R. Riudavets Puig, P. Boddie, and A. Mathelier.
BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences.
Bioinformatics btaa928 (2020).
:: DESCRIPTION
ModelGenerator is a model selection program that selects optimal amino acid and nucleotide substitution models from Fasta or Phylip alignments. ModelGenerator supports 56 nucleotide and 96 amino acid substitution models.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Thomas M Keane, Christopher J Creevey ,Melissa M Pentony, Thomas J Naughton and James O McInerney (2006)
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified,
BMC Evolutionary Biology, 6:29
