SelectSequencesFromMSA alternatives and similar packages

Based on the "Bioinformatics" category.
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hemokit

8.4 0.0 SelectSequencesFromMSA VS hemokit

Haskell library for the Emotiv EEG, inspired by the Emokit code
cobot

7.7 1.8 SelectSequencesFromMSA VS cobot

Computational biology toolkit to collaborate with researchers in constructive protein engineering

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cobot-io

7.4 5.1 SelectSequencesFromMSA VS cobot-io

Biological data file formats and IO
hPDB

7.2 0.0 SelectSequencesFromMSA VS hPDB

PDB parser in Haskell
samtools

6.8 0.0 SelectSequencesFromMSA VS samtools

DISCONTINUED. [Moved to: https://github.com/ingolia/SamTools]
RNAlien

6.6 0.0 SelectSequencesFromMSA VS RNAlien

RNAlien - unsupervised RNA family model construction
phybin

5.8 0.0 SelectSequencesFromMSA VS phybin

Binning (Newick) Phylogenetic Trees by Topology
bioinformatics-toolkit

5.7 0.0 SelectSequencesFromMSA VS bioinformatics-toolkit

A collection of bioinformatics algorithms
Genbank

5.6 0.0 SelectSequencesFromMSA VS Genbank

Genbank format tools and parser
BlastHTTP

5.3 0.0 SelectSequencesFromMSA VS BlastHTTP

Haskell cabal libary for submission and result retrieval from the NCBI Blast REST webservice
cmv

5.3 0.0 SelectSequencesFromMSA VS cmv

Visualize HMMs, CMs and their comparisons
vcf

5.3 0.0 SelectSequencesFromMSA VS vcf

Haskell library to handle VCF (Variant Call Format) files
FormalGrammars

5.1 0.0 SelectSequencesFromMSA VS FormalGrammars

Context-free and linear grammars in Haskell (parsing, pretty-printing, embedded DSL)
EntrezHTTP

5.0 0.0 SelectSequencesFromMSA VS EntrezHTTP

Haskell cabal libary for submission and result retrieval from the NCBI Entrez REST webservice
cobot-tools

5.0 3.6 SelectSequencesFromMSA VS cobot-tools

DISCONTINUED. Biological data file formats and IO
TaxonomyTools

4.1 0.0 SelectSequencesFromMSA VS TaxonomyTools

Tools to process and visualize NCBI taxonomy data
Taxonomy

3.9 0.0 SelectSequencesFromMSA VS Taxonomy

Haskell cabal Taxonomy libary contains tools, parsers, datastructures and visualisation for the NCBI (National Center for Biotechnology Information) Taxonomy datasources.
ClustalParser

3.6 0.0 SelectSequencesFromMSA VS ClustalParser

Parse output of Clustal tools
BioHMM

3.4 0.0 SelectSequencesFromMSA VS BioHMM

Libary containing parsing and visualisation functions and datastructures for Hidden Markov Models in HMMER3 format.
ViennaRNAParser

3.4 0.0 SelectSequencesFromMSA VS ViennaRNAParser

Libary for parsing ViennaRNA package output
memexml

3.4 0.0 SelectSequencesFromMSA VS memexml

Haskell cabal libary for parsing Meme motif finder xml output
StockholmAlignment

3.4 0.0 SelectSequencesFromMSA VS StockholmAlignment

Libary containing parsing and visualisation functions and datastructures for Stockholm aligmnent format.
Forestry

2.2 0.0 SelectSequencesFromMSA VS Forestry

Science and craft of forests
ADPfusionForest

1.9 0.0 SelectSequencesFromMSA VS ADPfusionForest

Dynamic programming on tree and forest structures
seqloc

1.9 0.0 SelectSequencesFromMSA VS seqloc

Bio.SeqLoc
Gene-CluEDO

1.9 0.0 SelectSequencesFromMSA VS Gene-CluEDO

Gene Cluster Evolution Determined Order
MutationOrder

1.7 0.0 SelectSequencesFromMSA VS MutationOrder

most likely order of mutation events in RNA
rank-product

1.6 0.0 SelectSequencesFromMSA VS rank-product

Collects the functions pertaining to finding the rank product of a data set as well as the associated p-value.
uniprot-kb

1.3 0.0 SelectSequencesFromMSA VS uniprot-kb

UniProt-KB format parser
mmtf

0.6 0.0 SelectSequencesFromMSA VS mmtf

MMTF for Haskell
bio-sequence

- - SelectSequencesFromMSA VS bio-sequence

DISCONTINUED. Initial project template from stack

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README

SelectSequencesFromMSA

SelectSequences is a tool for selection of a represenative subset of sequences from a multiple sequence alignment in clustal format. It is inspired the SelectSequences.pl script provided by RNAz.

It is available as a commandline tool only.

Installation via bioconda

SelectSequences can be installed with all dependencies via conda. Once you have conda installed simply type:

     conda install -c bioconda selectsequences

Available as docker container

SelectSequences is available with all dependencies via biocontainer. Install docker

     docker pull quay.io/biocontainers/selectsequences:1.0.0--pl5.22.0_0
     docker run -i -t quay.io/biocontainers/selectsequences:1.0.0--pl5.22.0_0 bash

Installation via cabal-install

SelectSequences is implemented in Haskell and can be installed via the Haskell package distribution sytem cabal. Once you have cabal installed simply type:

     cabal install SelectSequences

### Precompiled Executables

*   Archlinux (ghc-8.0.1) [SelectSequences 1.0.0 x86_64](http://www.bioinf.uni-freiburg.de//~egg/SelectSequences/archlinux-ghc8.0.1/SelectSequences-1.0.0)