Ideally I would like to use homoplasyFinder to identify convergent Amino Acid changes as well as nucleotide changes. This is one goal of the code overhaul that is in progress. The code overhaul is changing so INDELs and nucleotide mutations can be recorded in the same objects and analysed with the same methods. To do this, I am removing the reliance on defining the number of states - instead this is derived by the alignment or presence/absence table.
At the moment the initial overhaul is complete but it is now slower than the original homoplasyFinder - I need to work out any inefficiencies that have been introduced to bring the speed down. Don't think I can release until speed is the same or faster than original tool.
Ideally I would like to use homoplasyFinder to identify convergent Amino Acid changes as well as nucleotide changes. This is one goal of the code overhaul that is in progress. The code overhaul is changing so INDELs and nucleotide mutations can be recorded in the same objects and analysed with the same methods. To do this, I am removing the reliance on defining the number of states - instead this is derived by the alignment or presence/absence table.
At the moment the initial overhaul is complete but it is now slower than the original homoplasyFinder - I need to work out any inefficiencies that have been introduced to bring the speed down. Don't think I can release until speed is the same or faster than original tool.