<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/37239?offset=730 https://bioinformaticsonline.com/bookmarks/view/42826/ktrim-an-extra-fast-and-accurate-adapter-and-quality-trimmer-for-sequencing-data Thu, 11 Feb 2021 21:39:05 -0600 https://bioinformaticsonline.com/bookmarks/view/42826/ktrim-an-extra-fast-and-accurate-adapter-and-quality-trimmer-for-sequencing-data <![CDATA[Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data]]> Ktrim is written in C++ for GNU Linux/Unix platforms. After uncompressing the source package, you can find an executable file ktrim under bin/ directory compiled using g++ v4.8.5 and linked with libz v1.2.7 for Linux x86_64 system. If you could not run it (which is usually caused by low version of libc++ or libz library) or you want to build a version optimized for your system, you can re-compile the programs:

user@linux$ make clean && make

Address of the bookmark: https://github.com/hellosunking/Ktrim

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36017/alpha-a-toolkit-for-automated-local-phylogenomic-analyses Wed, 21 Mar 2018 18:12:06 -0500 https://bioinformaticsonline.com/bookmarks/view/36017/alpha-a-toolkit-for-automated-local-phylogenomic-analyses <![CDATA[ALPHA: A Toolkit for Automated Local Phylogenomic Analyses]]> Automated Local Phylogenomic Analyses, or ALPHA, is a python-based application that provides an intuitive user interface for phylogenetic analyses and data visualization. It has four distinct modes that are useful for different types of phylogenetic analysis: RAxML, File Converter, MS Comparison, and D-statistic.

Address of the bookmark: https://github.com/chilleo/ALPHA

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43445/parebrick-parallel-rearrangements-and-breaks-identification-toolkit Fri, 08 Oct 2021 10:20:03 -0500 https://bioinformaticsonline.com/bookmarks/view/43445/parebrick-parallel-rearrangements-and-breaks-identification-toolkit <![CDATA[PaReBrick: PArallel REarrangements and BReaks identification toolkit]]> PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. The tool provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved.We demonstrated PaReBrick’s efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes

More at https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btab691/6380551

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Address of the bookmark: https://github.com/ctlab/parallel-rearrangements

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