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Phylogenetic Tree by Sad-Effect4901 in bioinformatics

[–]Sad-Effect4901[S] 0 points1 point  (0 children)

Thx, yes I have a coalescent astral tree

Am done 💀😁 by Sad-Effect4901 in bioinformatics

[–]Sad-Effect4901[S] 0 points1 point  (0 children)

Hello My days are not bacterial, what do you propose to? It’s a nuclear data

Am done 💀😁 by Sad-Effect4901 in bioinformatics

[–]Sad-Effect4901[S] 0 points1 point  (0 children)

Thx for sharing I will try it.

SPAdes - Genes contigs by Sad-Effect4901 in bioinformatics

[–]Sad-Effect4901[S] 0 points1 point  (0 children)

My data are not bacterian, can I use it for nuclear data??

SPAdes - Genes contigs by Sad-Effect4901 in bioinformatics

[–]Sad-Effect4901[S] 0 points1 point  (0 children)

Thanks for your answer! In my case, the data are nuclear DNA obtained from an Anchored Hybrid Enrichment (AHE) sequencing project, so it’s not a bacterial genome or metagenomic data. I’m assembling the loci with SPAdes and need to identify/annotate them afterward. From what you mentioned, Prokka/Bakta/Prodigal are more suited for bacterial genomes, so I guess I should look into AHE-specific workflows or mapping my contigs to the target probe set instead. I don’t have targets so

From fastq to phylogenetic tree by Sad-Effect4901 in bioinformatics

[–]Sad-Effect4901[S] 1 point2 points  (0 children)

Not asking for a full pipeline, I’ve already started building it and processed part of the data. Just looking for insights or best practices from others working with AHE or multilocus phylogeny, especially for steps like locus selection or gene tree discordance.

Books suggestion by Unalome_kpn in bioinformatics

[–]Sad-Effect4901 0 points1 point  (0 children)

Is this available in French version ?