nickjcroucher

Add recipe for 3seq - bioinformatics software for analysis of recombinant sequences: https://mol.ax/software/3seq/

Improve distance estimation

2

It may be worth testing whether corrections to the pairwise distances could be employed as described in https://gitlab.pasteur.fr/GIPhy/JolyTree, as we are now observing core Hamming distances >0.1; as an initial...

Update 3seq

2

Enable greater control of 3seq behaviour in conda environment

Accessing $HOME in activate.sh

4

I am trying to change a configuration file stored in $HOME when a conda environment is activated (script [here](https://github.com/nickjcroucher/bioconda-recipes/blob/update_3seq/recipes/3seq/activate.sh)): ``` #!/bin/bash PVALUE_TABLE="${PREFIX}/share/3seq/PVT.3SEQ.2017.700"; export HOME=`env | grep HOME | cut -d=...

Lineage model fitting - PopPUNK changes

2

- Relies upon https://github.com/bacpop/pp-sketchlib/compare/master...flexible_lineages?expand=1 - All lineage models should now work from a single sparse matrix with kNN nearest neighbours (N.B. I have not checked whether nearest neighbours of the...

Update to 3.4.3

1

- Allows for file names with spaces in (#394) - Fixes installation issues with `numba` (#395 and #396)