Ksrates：在Ks分布中确定全基因组复制相对于物种形成事件的位置。
ksrates: positioning whole-genome duplications relative to speciation events in KS distributions.
作者信息
Sensalari Cecilia, Maere Steven, Lohaus Rolf
机构信息
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium.
VIB Center for Plant Systems Biology, Ghent 9052, Belgium.
出版信息
Bioinformatics. 2022 Jan 3;38(2):530-532. doi: 10.1093/bioinformatics/btab602.
SUMMARY
We present ksrates, a user-friendly command-line tool to position ancient whole-genome duplication events with respect to speciation events in a phylogeny by comparing paralog and ortholog KS distributions derived from genomic or transcriptomic sequences, while adjusting for substitution rate differences among the lineages involved.
AVAILABILITY AND IMPLEMENTATION
ksrates is implemented in Python 3 and as a Nextflow pipeline. The source code, Singularity and Docker containers, documentation and tutorial are available via https://github.com/VIB-PSB/ksrates.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
我们展示了ksrates，这是一个用户友好的命令行工具，通过比较从基因组或转录组序列中得出的旁系同源基因和直系同源基因的Ks分布，同时针对所涉及谱系间的替换率差异进行调整，从而在系统发育中确定古代全基因组复制事件相对于物种形成事件的位置。
可用性与实现方式
ksrates是用Python 3实现的，并作为一个Nextflow管道。源代码、Singularity和Docker容器、文档及教程可通过https://github.com/VIB-PSB/ksrates获取。
补充信息
补充数据可在《生物信息学》在线版获取。
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