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681. BEST
Bayesian Estimation of Species Trees works with Mr Bayes (see below).
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682. Bioconductor
A large collection of packages used within R for carring out very many functions in the analysis and comprehension of high-throughput genomic data.
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683. biogrep
Optimised version of grep for matching patterns against sequences.
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684. boxshade
Makes shaded multiple alignment files
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685. CAF tools
Suite of programs for manipulating CAF (Common Assembly Format) sequence assemblies
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686. cap3
Sequence assembly program DNA Sequence Assembly Program DNA Sequence Assembly Program
標(biāo)簽：de-novo assembly
687. CEGMA
Pipeline that identifies a core set of eukaryotic genes. It uses WU-BLAST, HMMER 2, geneid and Wise2. This may help check the completeness of a genome assembly. It could be used to train eg snap. May be used in conjunction with Maker. Local wrapper command?run_cegma?takes same arguments...
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688. clump
Program using Monte Carlo method for assessing significance of case-control association studies with multi-allelic markers. Installed for use on CamGrid
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689. clumpp
A program that deals with label switching and multimodality problems in population-genetic cluster analyses. Command?clumpp
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690. clustal
Multiple sequence alignment;?clustalw2?is the current version.?clustalx2?is an?X-Windows?version.?clustalo?is special new fast version for proteins only.
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691. CNS
CNS (Crystallography and NMR System) is a program for macromolecular structure determination
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692. consed
A viewer for files made by phrap and an editor for these assemblies. Requires?X-windows.
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693. Consensus
Program to find the consensus in unaligned sequences This program determines consensus patterns in unaligned sequences. The algorithm is based on a matrix representation of a consensus pattern. This program determines consensus patterns in unaligned sequences. The algorithm is based o...
標(biāo)簽：Sequence motif discovery
694. densitree
Program for qualitative analysis of sets of trees.
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695. DL_POLY
A package for molecular dynamics simulations
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696. dotter
A graphical dotplot program for detailed comparison of two sequences; Requires?X-Windows
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697. eigensoft
Programs related to ancestrymap (see above) from the Reich Lab for studying human history, evolution and disease gene mapping
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698. EMBOSS
The European Molecular Biology Open Software Suite version 6.3.1 is available. Type?emboss6?to over-ride use of version 5 installed with the operating system. EMBOSS (European Molecular Biology Open Software Suite) is a new suite of freely available programs and libraries for sequence ...
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699. FAR
Flexible adapter remover software using Needleman Wunsch alignment. Works on many formats of sequencing reads. Command?far
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700. FASTA (including SSEARCH etc)
Sequence database searching package. Slower than blast. May be most useful for some protein searches.
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