For some weeks I'm fighting with an issue about phylogenetic tree building to use in a phyloseq object in order to calculate beta-diversity metrics that takes into account phylogenetic distance.
I’m trying to create a phylogenetic tree from the representative genomes of proGenomes v.2.1 database. However, I do not have a representative genome for each taxa id. In contrast, I have a multifasta files for more than 100 contigs for each taxa ID (file freeze12.contigs.representatives.fasta.gz).
For each taxaID (the first numbers in each header of the multifasta file is NCBI taxon ID), I would like to bin the contigs into the biggest scaffold possible, and then perform an alignment (through MUSCLE as examples) followed by RaXML-NG to construct a Newick tree.
However, I cannot find any software for binning contigs with only the contigs as inputs. MetaBAT needs bam files from shotgun read mappings to the contigs in question (not present in the proGenomes database). I found another software (Scaffold_builder), but it needs a representative reference genome. And in microbiology I have more than 100 complete genomes for each NCBI tax id...
For this reason, I ask here an open question if exists some software that can perform of contigs taking into account only a multifasta file of contigs?