homoplasyFinder

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Problem using readAnnotatedTree function

1

Hi, First of all, thank you very much for the package. I'm trying to use it with my data. I was able to generate the results table. However, when I...

BioinfoNovice

R Session Aborted

2

I think the `R Session Aborted` error is caused by `homoplasyFinder` hanging after an error has been introduced. See the image below, I introduced an error by sending the wrong...

JosephCrispell

Hi Joseph, Thanks for your program, it is very fast and convenient! I am trying to use it to classify some mutations which I added to a presence absence file....

tamaraprieto

At the moment declaring boolean arrays of length 4 to store state presence at lines 508 and 511 in [ConsistencyIndex.java](https://github.com/JosephCrispell/Java/blob/master/HomoplasyFinder/src/homoplasyFinder/ConsistencyIndex.java). Should use the `comparePossibleStatesOfTwoSubNodes()` function's `nStatesPerSite` parameter instead of hard...

JosephCrispell

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....

JosephCrispell

Output inconsistent sites as VCF file

3

An important enhancement pointed out by [flashton2003](https://github.com/flashton2003). Thanks! Include option in `homoplasyFinder` to export the `consistencyIndexReport_DATE.txt` file in a VCF file format. The VCF file can then easily be run...

JosephCrispell

Could not run homoplasyFinder R

1

Hello, I am trying to run homoplasyFinder (R) on set of whole genome multi-fasta alignment. The file have gaps. I run to the following error. If feedback on the wright...

hmamine