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debugging tricky phylogeny problems

Debugging stuff

Imported from a comment discussion on https://bioinformatics.stackexchange.com/questions/22873/combing-multiple-sra-runs-into-a-single-sample-biosample-or-library

Imported from a comment discussion on https://bioinformatics.stackexchange.com/questions/21108/singularity-and-macos/21109#21109

Imported from a comment discussion on https://bioinformatics.stackexchange.com/questions/20931/how-can-i-make-this-biopython-program-to-correct-erroneous-barcodes-run-faster

Imported from a comment discussion on https://bioinformatics.stackexchange.com/questions/20834/gatk-g-cnv-singularity-and-a-peculiar-error-fatal-executable-file-not-f

Imported from a comment discussion on https://bioinformatics.stackexchange.com/questions/20792/manta-exome-command-not-found/20793#20793

Imported from a comment discussion on https://bioinformatics.stackexchange.com/questions/20596/delete-each-blocks-of-lines-if-the-results-of-xyz-coordinates-are-bigger-than-40

Imported from a comment discussion on https://bioinformatics.stackexchange.com/questions/20314/sanger-sequencing-annotation-error

Imported from a comment discussion on https://bioinformatics.stackexchange.com/questions/18859/how-can-i-separate-upregulated-genes-from-downregulated-on-a-boxplot

Imported from a comment discussion on https://bioinformatics.stackexchange.com/questions/15953/retain-only-part-of-a-file-name-and-fasta-header-in-fasta-directory/15956#15956

Imported from a comment discussion on https://bioinformatics.stackexchange.com/questions/15704/snpeff-not-correctly-annotating-multiple-nucleotide-polymorphisms

Imported from a comment discussion on https://bioinformatics.stackexchange.com/questions/14520/genome-assembly-of-srr12196449-with-spades/14606#14606

Imported from a comment discussion on https://bioinformatics.stackexchange.com/questions/14520/genome-assembly-of-srr12196449-with-spades/14606#14606

Imported from a comment discussion on https://bioinformatics.stackexchange.com/questions/14125/interpreting-this-plot-from-gsea

Imported from a comment discussion on https://bioinformatics.stackexchange.com/questions/13859/what-is-the-pvalue-from-anovaglm1-glm2-test-chisq-telling-me-in-r-when-t

Imported from a comment discussion on https://bioinformatics.stackexchange.com/questions/13556/finding-out-group-in-unrooted-tree/13557#13557

Imported from a comment discussion on https://bioinformatics.stackexchange.com/questions/13403/adding-external-annotation-to-the-phylogeny-tree/13409#13409

Imported from a comment discussion on https://bioinformatics.stackexchange.com/questions/13377/comparing-phylogeny-in-r/13378#13378

Imported from a comment discussion on https://bioinformatics.stackexchange.com/questions/13013/why-is-libraryseurat-causing-my-r-session-to-have-a-fatal-error

Imported from a comment discussion on https://bioinformatics.stackexchange.com/questions/8767/bcl2fastq2-v2-20-0-converstion-software-on-ubuntu-18-04

Imported from a comment discussion on https://bioinformatics.stackexchange.com/questions/7340/how-to-predict-stop-codons-in-illumina-reads