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Notes from the workbench — mathematics, algorithms, and computational biology.

A place for worked examples, notebooks, and ideas worth keeping.

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Personal

On keeping a lasting record of ideas and conversations.

5 Jan 2026

Welcome

Misc

A brief introduction and a new chapter in Liverpool.

4 Jan 2026

Not all invariant sites are created the same

phylogenetics

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

16 Aug 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.

1 Apr 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.

1 Mar 2022

Minimal example of a rolling hash

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

1 Feb 2022

Quantile functions implemented in biomcmc-lib

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

1 Jan 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.

1 Dec 2021

Welcome to the blog

random

The beginning of Binfie Notes, with an update from Liverpool.

1 Jan 2018

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