I have just updated and restructured my long reference blog post on species tree methods. The occasion is that I have tried out ASTRAL for the first time today, so I decided to add it to the list.
TL;DR:
The only inputs are a text file with all the gene trees in Newick format and, if there are multiple alleles per species, an allele assignation table. In that case, also make sure to download the "multiple individuals" version here instead of the master version. The program needs Java and is run through the command line.
ASTRAL is fast and very flexible, and the results I got are meaningful although without branch lengths, limiting the downstream use cases. It is available for all three major operating systems and worked seamlessly on my Linux computer.
Downsides are the aforementioned command line operation, at least for people who are unfamiliar with that, and in my eyes the feeling that the developers are uncomfortable with and may not trust their current multiple individuals version ("The code for handling multiple individuals is in its infancy and might not work well yet").
Apart from adding ASTRAL and iGTP, I reorganised the long blog post to be a list of software tools in contrast to a list of methods. I hope it will continue to be useful to people searching the internet for an overview and comparison of species tree methods.
The blog of a systematic botanist of German origin, now working in Australia. It covers botany, phylogenetics, cladistics, science in general, freethought, and occasionally sillier issues.
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