<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/33924?offset=30 https://bioinformaticsonline.com/bookmarks/view/42794/tmrca-calculator Wed, 03 Feb 2021 05:07:30 -0600 https://bioinformaticsonline.com/bookmarks/view/42794/tmrca-calculator <![CDATA[TMRCA Calculator]]> This program calculates the probability that two people have a certain number of generations between them, based on the standard infinite alleles formula of Walsh. It calculates both the probability of being at an exact number of generations back to the Most Recent Common Ancestor (MRCA) of a certain pair of people and the cumulative probability that the actual number of generations is less than a certain value. Note that the convention using generations is changed from an earlier version of this calculator which used "transmission events". It can list both result types in a table or graph. In either case the horizontal axis stops at the point where the cumulative probability reaches 95% or 10 generations, whichever is longer, or an absolute max of 50,000. Beyond 90% the calculation becomes inaccurate.

https://clandonaldusa.org/index.php/tmrca-calculator

Address of the bookmark: https://clandonaldusa.org/index.php/tmrca-calculator

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/44513/mike-an-ultrafast-assembly-and-alignment-free-approach-for-phylogenetic-tree-construction Mon, 08 Apr 2024 06:19:52 -0500 https://bioinformaticsonline.com/bookmarks/view/44513/mike-an-ultrafast-assembly-and-alignment-free-approach-for-phylogenetic-tree-construction <![CDATA[MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction]]> MIKE (MinHash-based k-mer algorithm). This algorithm is designed for the swift calculation of the Jaccard coefficient directly from raw sequencing reads and enables the construction of phylogenetic trees based on the resultant Jaccard coefficient. Simulation results highlight the superior speed of MIKE compared to existing state-of-the-art methods. We used MIKE to reconstruct a phylogenetic tree, incorporating 238 yeast, 303 Zea, 141 Ficus, 67 Oryza, and 43 Saccharum spontaneum samples. MIKE demonstrated accurate performance across varying evolutionary scales, reproductive modes, and ploidy levels, proving itself as a powerful tool for phylogenetic tree construction.

Address of the bookmark: https://github.com/Argonum-Clever2/mike

]]> Abhi