liamfriar

Hi. I am struggling to find instructions or examples for how to color a plot using the command line Krona tools. For instance, I have two metagenomic samples for which...

Using Nucleotide vs Amino Acid fastas as input

1

Hi, Thank you for building this tool. It is really great and quite user friendly. What are the advantages or disadvantages of using nucleotide sequences as the input to orthofinder...

Has anyone tested if MITObim has a bias against genomic rearrangements relative to the reference given? I want to use MITObim to try to circularize a bacterial genome that SPAdes...

No summary file

3

Hi, I am using the following call to spray-and-pray.py: ` spray-and-pray.py -t 20 --euk --meta --spades -bam ${prefix}.pairedReads2assembly.sorted.bam -g $file -ref /home/liam/data/nr/nr.dmnd -out spraynpray_out/$bin` I am receiving the following error....

label-tree.bf is rerooting trees when I do not want it to

3

[N9.HOG0000289_tree.labeled.txt](https://github.com/veg/hyphy-analyses/files/13653348/N9.HOG0000289_tree.labeled.txt) [N9.HOG0000289.pruned_tree.txt](https://github.com/veg/hyphy-analyses/files/13653349/N9.HOG0000289.pruned_tree.txt) [test_list.txt](https://github.com/veg/hyphy-analyses/files/13653353/test_list.txt) Input and output files are attached. The function call is below. Maybe I could use the `--reroot` flag and give it the original root, but I just...