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License: GNU General Public License v3.0
Goldfinder detects gene co-occurrence and avoidance accounting for phylogenetic relationships
License: GNU General Public License v3.0
The current method to infer a tree from the presence and absence matrix is suboptimal and should be replaced with a more suitable distance function. I would suggest we use the distance from https://doi.org/10.1093/bioinformatics/bth198
However, the recommended way to use Goldfinder is to use it with a user-provided tree.
Refer to output in screenshot. It's caused if the Gene
, Non-unique Gene name
and Annotation
columns in the roary-outputted gene_presence_absence.csv
file contain one or more commas (e.g. if you've pulled annotations direct from Prokka or Bakta gff files when creating the pangenome). Get rid of the problem commas and it runs fine.
Posting this here in cases others come across the same issue.
We are currently missing an option to read in standard csv files with 0s and 1s for the presence and absence of genes/features.
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