antoine

Hello I have a big tree (n=29k tips) from which I would like to highlight some clades I defined those clades in the meta which looks like that:  ```...

shift in annotated AA position

1

Hi All, After importing codeml_tree from codon based alignment, I tried to add annotation of amino acid substitution inferred by joint probabilities with the following command: merged_tree

Hello I am trying to subsample fastq.gz file but not sure if it really works as expected above a given limit. my source file contains 150k reads ``` awk '{s++}END{print...

Hello I am trying to combine 2 plots but I need to adjust the position of the bottom plot to be aligned with position 1 of the x axis of...

rarefaction analyses and sampling depth

1

hello thank you for all these great tools. would it be possible to generate rarefaction curve to assess sampling depth (e.g. by subsampling data without replacement at XXX sequence increments,...

medaka versions Mac vs Linux

1

hello I am trying to run medaka on my mac installed successful with conda BUT latest version is ``` This is medaka 1.0.3 Program Version Required Pass bcftools 1.10.2 1.9...

microbiome decontamination

2

Hello I am looking for advices for the best way to clean up microbiome sequencing data that have been contaminated by Mock community (Zymo) controls. I know how many cells...

Hello I am trying to run freebayes (as part of snippy) but get this error I do have vcflib isntalled in my env /opt/miniconda3/envs/instaflu_env/bin/freebayes-parallel: line 40: 1655 Done ( cat...

Hello thank you for this nice package. it is exactly what I was looking for with one limitation.. I have a dataset made of 6 lists of overlapping genes across...

failed to fetch

7

Hello I just installed the 2 required packages and tried to fetch a couple of refs (using either my PMID or the example_pmf.tsv) but I get the following errors: Any...