6255 gene alignments of Asellidae CDS

Families of orthologous genes used in "No evidence that nitrogen limitation influences the elemental composition of isopod transcriptomes and proteomes"

The 6,255 alignments used in this publication are archived here. Each alignment corresponds to one "pattern" (~ gene family, except when one family X is composed of several patterns = e.g. multigenic family). Each alignment includes between 2 and 26 species. These alignments have been created with:

• prank -codon -F
• GBlocks -b5=h (to allow some gaps)

Alignment are named according to the corresponding family_pattern, e.g. "FAM003424_1.fas.prank_codon.best.fas-gb.bis" corresponds to the family "003424" and the pattern "1". They are composed of several fasta sequences, each sequence corresponding to one species. The name of each fasta sequence starts with the species code (e: BMOV, PCANC) in upper letters. Gaps are present ("----"). ATTENTION: species order differs in each alignment!

Table of the correspondance species - code:

Species                     Code     couple    eco
P. beticus                   PBTS    c1    epi
P. jaloniacus              PJJ       c1    hypo
P. aragonensis          PARE    c2    epi
P. spelaeus               PSSE    c2    hypo
B. peltatus                BPM      c3    epi
B. molinai                 BMOV   c3    hypo
P. ibericus                PIBB      c4    epi
P. arthrodilus            PATL     c4    hypo
P. meridianus           PMLL    c5    epi
P. margalefi              PMAF   c5    hypo
P. granandensis       PGRP   c6    epi
P. solanasi               PSOG   c6    hypo
P. coxalis                 PCOB   c7    epi
P. parvulus              PPRS    c7    hypo
P. assaforensis        PASA     c8    epi
P. rectus                  PRUE     c8    hypo
P. karamani             PKK        c9    epi
P. hercegovinensis  PHEZ     c9    hypo
P. coiffaiti                 PCOIP    c10    epi
P. cavaticus           PCBF      c10    hypo
P. racovitzai           PRBE     c11    epi
P. escolai               PECD     c11    hypo
P. ortizi                   POJ         c12    epi
P. grafi                   PGC         c12    hypo
P. ebrensis             PEF          c13    epi
P. cantabricus        PCANC    c13    hypo

Remark: out of these 6,255 alignments, 8 alignments are empty (when Gblock has removed ALL aligned positions): [1] "FAM000157_5.fas" "FAM000587_3.fas" "FAM000615_1.fas" "FAM008836_1.fas" [5] "FAM013862_1.fas" "FAM015586_1.fas" "FAM017544_1.fas" "FAM022381_1.fas"