Notes on Evolutionary Computational Biology and Bioinformatics. By Leonardo de Oliveira Martins.

Posts

• Not all invariant sites are created the same

  Why removing invariant sites is usually a bad idea for maximum likelihood tree inference

  Aug 16, 2022

• Hash functions and pseudo-random number generation

  Here I show two small tests, one with generation of an initial set of random numbers, and another on `popcount()` speeds, implemented in the low-level phylogenetic library biomcmc-lib.

  Apr 1, 2022

• kalign3 as a library and colour printing

  How the multiple sequence alignment kalign3 is implemented in the low-level phylogenetic library biomcmc-lib, and how to use colours in C.

  Mar 1, 2022

• Minimal example of a rolling hash

  Description of a current implementation of a rolling hash in the low-level phylogenetic library biomcmc-lib

  Feb 1, 2022

• Quantile functions implemented in biomcmc-lib

  Description of how quantile finding is implemented in the low-level phylogenetic library biomcmc-lib

  Jan 1, 2022

• K-mer in biomcmc-lib

  This notebook contains a few details of how kmers are implemented in the low-level phylogenetic library biomcmc-lib.

  Dec 1, 2021

• Welcome to the blog

  I am Leo Martins, a Computational Biologist at the Quadram Institute Biosciences.

  Jan 1, 2018