<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/35249?offset=230 https://bioinformaticsonline.com/bookmarks/view/32853/progressivecactus Thu, 18 May 2017 05:29:29 -0500 https://bioinformaticsonline.com/bookmarks/view/32853/progressivecactus <![CDATA[progressiveCactus]]> Progressive Cactus is a whole-genome alignment package.

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules

https://github.com/glennhickey/progressiveCactus

Address of the bookmark: https://github.com/glennhickey/progressiveCactus

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/40814/accesssyri-finding-genomic-rearrangements-and-local-sequence-differences-from-whole-genome-assemblies Sat, 01 Feb 2020 13:38:49 -0600 https://bioinformaticsonline.com/bookmarks/view/40814/accesssyri-finding-genomic-rearrangements-and-local-sequence-differences-from-whole-genome-assemblies <![CDATA[AccessSyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies]]> AccessSyRI: finding genomic rearrangements andlocal sequence differences from whole-genome assemblies

SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1911-0

Address of the bookmark: https://github.com/schneebergerlab/syri

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44479/doubletrouble-identify-duplicated-genes-from-whole-genome-protein-sequences-and-classify Tue, 05 Mar 2024 00:23:49 -0600 https://bioinformaticsonline.com/bookmarks/view/44479/doubletrouble-identify-duplicated-genes-from-whole-genome-protein-sequences-and-classify <![CDATA[doubletrouble: identify duplicated genes from whole-genome protein sequences and classify]]> doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a simpler classification scheme, duplicates can also be classified into SD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.

Address of the bookmark: https://bioconductor.org/packages/release/bioc/html/doubletrouble.html

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