Torsten Seemann

If you use the latest github HEAD I have changed some code to make smaller contig names. It might help when you use `--compliant` mode.

No rush - let's just wait until you have 1.5 (or 2.0) ready!

Those options cover most of what I asked, except for the alphabet. It does detect 'dna' in general, ``` % readal -type -in full.aln ## Input file datatype nucleotides:dna ```...

Thanks!

Thje documentation for v1.6 says it does handle IUPAC codes correcrtly. So I assume 2.x is the same.

No it stayed there for 20 hours without any output, but CPU cycles being chewed. I killed it. I'll try and reproduce it and send a log.

`--tbe` alone also adds no confidence values to the `.treefile` output

i was doing `-B 1000 --tbe`. Will use `-b` instead. thank you!

It was gcc-5.5.0 againt eigen 3.3.7 (using installed brew eigen3, hfd5 and htslib)

There is something strange with that line. DP=981 but DP4 does not add up to 981. Is this a SNP or an INDEL Please paste the WHOLE line from the...