Torsten Seemann

Argument "1.7.7" isn't numeric in numeric

18

Argument "1.7.7" isn't numeric in numeric lt (

Add information about plasmid annotation

9

For plasmid you will not get a good result if you just use the default settings. I would recommend getting GENBANK files (.gbk or .gb) of all the plasmids that...

Tag a new release?

2

Lots of commits since 1.4.1 ?

statal - basic report with #seq

2

Is there a way for `statal` to give me the basic information of - name of the alignment (if the format supports it) - number of entries - length of...

statal - alphabet distribution report

2

I deal a lot with core genome SNP alignments (DNA) across 100s of bacterial samples. A useful report would be like this: ``` ID #A #G #T #C #N #-...

Any plans for multi-threading support in trimAl ?

2

Are there any plans to support multi-threading? I understand it is not trivial to implement, but OpenMP pragmas could make it easy to parallelize parts of the code that loop...

identical sequences not getting brlen = 0

2

If you give iqtree 2.1.0 identical sequences Tjeu end up with a BL of 0.000001 I think thjis is a bug THis problem persisits even when --polyomy is used ALso,...

`Generating 98 parsimony trees... ` seems t o spend 1-2 hours on this stage single threaded only that''s ok - but jhave --vebrose on and i get no extra output...

IQTree --tbe never finishes running

2

It stays at this point forever: ``` CPUS=8 MODEL="GTR+F+R3" CONFIDENCE="-b 100 --tbe" iqtree2 -s $OUT.afa --seqtype DNA -o $REFID \ --prefix $OUT.iqtree \ -T $CPUS --redo --verbose \ $CONFIDENCE \...

warning: 'template<class _Operation> class std::binder2nd' is deprecated

3

FYI - vanilla 0.12.0 + recent commits (HEAD) ``` g++ -o src/nanopolish_methyltrain.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -I./include -I./htslib -I./minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model...