VESPA: Very large-scale Evolutionary and Selective Pressure Analyses
find the resources we provide here useful in getting you set up to analyse and interpret your data. To reference VESPA: https://peerj.com/preprints/1895/ Documentation is now hosted on ReadTheDocs1841 days ago
jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes...1807 days ago
Cactus: a reference-free whole-genome multiple alignment program
Cactus is a reference-free whole-genome multiple alignment program. The principal algori...ctus uses substantial resources. For primate-sized genomes (3 gigabases each), you shoul...uadratically, so aligning two 1-megabase bacterial genomes...1790 days ago
dnaPipeTE: a pipeline designed to find, annotate and quantify Transposable Elements
dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to fin...asets. It is very useful to quantify the proportion of TEs in newly sequenced genomes...1789 days ago
TRITEX sequence assembly pipeline for Triticeae genomes
The pipeline is open-source and hosted in a public Bitbucket repository. TRITEX has been run on highly...ever been tested and is not expected to work on heterozygous or autopolyploid genomes....1782 days ago
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MFannot : a program for the annotation of mitochondrial and plastid genomes
MFannot is a program for the annotation of mitochondrial and plastid genomes MFannot is a program for the annotation of mitochondrial and plastid genomes....1776 days ago
Miropeats: discovers regions of sequence similarity amongst any set of DNA sequences
Miropeats discovers regions of sequence similarity amongst any set of DNA sequences a...very general tool that forms the basis of many different biological sequence analyses but it is limited by the verb...1775 days ago
Retrieving Taxonomic Information with R
This vignette will introduce users to the retrieval of taxonomic information with myTAI. The taxonomy()&n...xonomy() function implemented in myTAI can be used to classify genomes...1773 days ago
ALF--a simulation framework for genome evolution.
Artificial Life Framework (ALF) simulates a root genome into a number of related genomes. Result files include the resulting gene sequences, true tree and true MSAs. A description of ALF can be...1718 days ago