761. Raster3D
Molecular graphics package
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762. RAxML
(Randomized accelerated Maximum Likelihood) program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees
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763. RepeatMasker
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the a...
标签:重复序列,基因组注释,推荐
764. RepeatScout
Software to identify repeat family sequences from genomes. Can use output as input to RepeatMasker.
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765. ROADTRIPS
Program that performs single-SNP, case-control association testing in samples with partially or completely unknown population and pedigree structure; command roadtrips
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766. SAM tools
SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
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767. Scilab
A package similar to Matlab for numerical computation
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768. seaview
Muliple alignment editor; requires X-Windows
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769. sff_extract
Extracts reads from 454 sff files and stores in fasta xml or caf text files.
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770. Shogun
A large-scale machine learning toolbox
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771. sigma
A program for aligning non-coding DNA
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772. SignalP
Predicts the presence and location of signal peptide cleavage sites in amino acids from different organisms. SignalP 4.1 predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokar...
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773. simwalk2
A statistical genetics application for haplotype, parametric or non-parameric linkage, identity by descent and mustyping analyses
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774. smoldyn
Program to perform cell-scale simulation, implemented on CamGrid.
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775. splink
Program for linkage analysis using affected sib pairs
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776. SRA toolkit
Set of programs for converting NCBI SRA archive format into various other formats.
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777. ssaha2
Package for mapping DNA sequencing reads onto a genomic reference sequence
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778. Stacks
Software pipeline for building loci out of a set of short-read sequenced samples. Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-se...
标签:Nucleic acid sequence analysis
779. strat
Companion software for structure (below).
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780. structure
Program that implements a model-based clustering method for inferring population structure using genotype data consisting of unlinked markers
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