Hello. I tried to do a similarity analysis of 8 species in JSpeciesWS because some genomes are fragmented so I couldn´t do It on MEGA. I don´t know if is posible doing a phylogenetic tree in R or something when the genomes are fragmented. The problem is that JSpeciesWS doesn´t do the same alignment to all genomes so the similarity percentages were weird and when I did the phylogenetic tree in R with the percentages matrix, It makes no sense. Is there any way to do the phylogenetic tree well? With some program or R. (The problem is the genomes that are fragmented)
Here you can see my genomes and how many fragments have each one:
https://gyazo.com/d52826a06555521a7c5c9c8141b3e304
Here you can see the percentage of similarity and the alignment of each one:
https://gyazo.com/1a37f0bacc5874721689eaeb250a1149
And here you can see the phylogenetic tree that doesn´t make sense to me:
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