-
I'm setting this to run in a genome-wide scan with 7 species and 13,000 genes (13k separate runs). Fairly naive question: how do I get a simple report of the genomes where positive selection is detec…
-
I keep getting the error below. Any clue?
treetime homoplasy --aln homoplasy_25807.fna --tree Multifasta_25807_aligned_.nwk --verbose 6
0.00 -TreeAnc: set-up
read alignment from file homoplasy_25…
-
Dear MBoemo
Thanks for this useful tool. I have installed this tool and used it several months before, and now I am re-installing and re-analyzing this data from GridION basecalled data. I got…
-
Hello!
I'm trying to write a new CGE library with different goals, but first I must understand the evaluation of CGE networks!
I am a little stuck in understanding how the topology of CGE networ…
-
`UCB_Xtro_10.0` is a [Western clawed frog](https://en.wikipedia.org/wiki/Western_clawed_frog) (_Xenopus tropicalis_) assembly available at NCBI: https://www.ncbi.nlm.nih.gov/assembly/GCF_000004195.4/
…
-
Our [latest database release is pretty nice](http://ivory.idyll.org/blog/2021-sourmash-new-databases.html), but life is also getting much more complicated ;). The process @bluegenes (mostly) and I are…
-
Hey, great tool! Looks very promising to combine it with RepeatMasker gff3 annotation, and I love the way of installation - so easy! Every python program should do this!
So I tried it on a 44K-sequ…
-
Hi,
I am trying to use GRAFIMO to scan multiple motifs in a genome graph.
I passed in a MEME file with roughly 300 motifs defined in it.
The tools works fine, but every time it finishes with one …
-
Similar issue for me. Bactopia worked well in 1.7.0 but always failed in the steps of 'ASSEMBLE_GENOME' and 'ARIBA_ANALYSIS' in 2.0.0.
I worked in the conda environment in a macOSX machine.
Err…
-
Currently, the hmmer searches executed by the `progenomics search` task often don't make full use of the requested cpus. A possible reason could be that genomes are scanned individually against a prof…