Chris Wymant

Thanks very much for the more complete installation instructions! I'm afraid I have neither experience with Docker nor the time available to do this in the short term, though it...

Hi Kurtman, indeed shiver requires Python2, not Python3. Within your Python2 installation, certain modules are required including Biopython. If you have multiple Python2 installations on your machine, the one shiver...

I've not previously had a problem running both python2 and python3 on the same machine, though I'm far from an expert on conda and having different environments etc. An alternative...

Hi Evan, the only method of bootsrapping with which I am familiar is to bootstrap the alignment, and then calculate a tree from each alignment in the usual way. I...

"When I use that option" - I assume you mean `--no-trees`? This option means RAxML is not run, i.e. `phyloscanner_make_trees.py` only produces an alignment file in each window. You then...

Hi Simon, all of the python/bioinformatic part of phyloscanner is designed & structured around the idea that each file of mapped reads has only one reference, because we consider it...

I've never worked with multi-chromosome / fragmented data so I'm not sure how exactly the mapping process worked, but I'm assuming the process results in a bam file in which...

That's mysterious, it looks like RAxML is failing without saying why. Have you printed the whole phyloscanner output above or just part of it? Having the whole output message might...

OK, with regards to the first bit - `Warning: RAxML files are present in the working directory. If their names clash with those that phyloscanner will try to create, RAxML...

Strange. See this suggestion: >Can you try running RAxML manually on the reads in that window? e.g. with `raxmlHPC -m GTRCAT -p 1 --no-seq-chec -s AlignedReads/AlignedReadsInWindow_8000_to_8299.fasta -n my_output_label` specifying the...