<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/44633?offset=80 https://bioinformaticsonline.com/bookmarks/view/41459/jcvipython-utility-libraries-on-genome-assembly-annotation-and-comparative-genomics Tue, 17 Mar 2020 06:19:06 -0500 https://bioinformaticsonline.com/bookmarks/view/41459/jcvipython-utility-libraries-on-genome-assembly-annotation-and-comparative-genomics <![CDATA[JCVI:Python utility libraries on genome assembly, annotation and comparative genomics]]> Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

https://github.com/tanghaibao/jcvi

More at https://github.com/tanghaibao/jcvi/wiki

Address of the bookmark: https://github.com/tanghaibao/jcvi

]]> Jit https://bioinformaticsonline.com/bookmarks/view/34567/jobtree-based-python-wrapper-to-run-the-genome-simulation-tool-suite-evolver Fri, 08 Dec 2017 16:26:32 -0600 https://bioinformaticsonline.com/bookmarks/view/34567/jobtree-based-python-wrapper-to-run-the-genome-simulation-tool-suite-evolver <![CDATA[jobTree based python wrapper to run the genome simulation tool suite Evolver]]> evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolver, eSC also automatically creates statistical summaries of the simulation as it runs including text and image files. Also included are convenience scripts to: check on a running simulation and see detailed status and logging information; extract fasta sequence files from the leaf nodes of a completed simulation; extract pairwise multiple alignment files (.maf) from leaf and branch nodes from a completed simulation and with the help of mafJoin, join them together into a single maf covering the entire simulation.

Address of the bookmark: https://github.com/dentearl/evolverSimControl

]]> Jit https://bioinformaticsonline.com/bookmarks/view/40099/contiguator Fri, 04 Oct 2019 01:27:58 -0500 https://bioinformaticsonline.com/bookmarks/view/40099/contiguator <![CDATA[CONTIGuator !]]> CONTIGuator is a Python script for Linux environments whose purpose is to speed-up the bacterial genome assembly process and to obtain a first insight of the genome structure using the well-known artemis comparison tool (ACT).

 

Address of the bookmark: https://sourceforge.net/projects/contiguator/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/44373/mitohifi-a-python-pipeline-for-mitochondrial-genome-assembly-from-pacbio-high-fidelity-reads Tue, 05 Sep 2023 07:31:35 -0500 https://bioinformaticsonline.com/bookmarks/view/44373/mitohifi-a-python-pipeline-for-mitochondrial-genome-assembly-from-pacbio-high-fidelity-reads <![CDATA[MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads]]> MitoHiFi v3.2 is a python pipeline distributed under MIT License !

MitoHiFi was first developed to assemble the mitogenomes for a wide range of species in the Darwin Tree of Life Project (DToL)

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05385-y 

Address of the bookmark: https://github.com/marcelauliano/MitoHiFi

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