Query : Tool [subsection]
ElandToFastq |
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Reads summary statistics |
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Transalign |
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Multiple alignment of protein-coding DNA sequences : Facilitates the multiple alignment of protein-coding DNA sequences by aligning the amino acids sequences they specify.
Author(s)Bininda-Emonds
1
BppGenDist |
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BppPermGenDist |
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Mantel Test |
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Samtools Flag Filter |
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Readseq was written originally around 1989 a component of a sequence analysis program, but when I added a small, simple command-line interface, it took on a life of its own as a conversion program for bioinformatics. It's main contribution to bioinformatics is it takes on the job of guessing what your input biosequence data format is, and converting it to what your software knows how to handle.
Author(s)D. Gilbert
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Reads simulator |
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wgsim simulator program from samtools
Author(s)Heng Li
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This procedure is aimed to reduce the dimensionality of a genotypic data to visualize them in a subspace of 2 or 3 dimensions. Adapted from ca R-package by Nenadic and Greenacre. Pseudo-individus are constructed for each population by summing individual alleles counts. These values are then added to the matrix of individual alleles and analysed with ca() while setting only the pseudo-individus as active elements.
Author(s)Unknown
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IDxen upload |
Alignment  permalink |
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Tool to upload new reference versions to IDxen.
Author(s)Julien Veyssier
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Alignment - Phylogenetic reconstruction - Pipeline - Tool
Magic-BLAST |
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This interactive application is an R shiny wrapper around the SIMRAD package. Given a particular genome, the user can simulate an inSillico RAD sequencing experiment. Interactively playing with different parameters including fragments size and Restriction enzymes one can assess the amount of sequencing runs needed for a multiplexing design and an expected coverage.
Author(s)BELKHIR
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PopPhyl |
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The PopPhyl project provides a set of publicly available tools C++ code to achieve SNP and genotype calling (with home made algorithms). Also are provided wrappers to use this tools in the Galaxy platforms.
Executables tools
Nicolas Galtier et al.
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Linux - Windows - Mac
Yes
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