5/21/22, 3:07 PM Multiple sequence alignment by MAFFT ver.

LAST hits (score>39) between Clustal format

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Reformat to GCG, PHYLIP, MSF, NEXUS,
uppercase/lowercase, etc. with Readseq

GUIDANCE2 computes the residue-wise confidence scores

and extracts well-aligned residues.

Refine dataset

Phylogenetic tree

MAFFT-L-INS-i Result

CLUSTAL format alignment by MAFFT (v7.505)

Phalaenopsis_ch tacaacatatattactgtcaagagaggggacc
Phalaenopsis_su tacaacatatattactgtcaagagaggggacc
Phalaenopsis_ja tacaacatatattactgtcaagagaggggacc
Phalaenopsis_in tacaacatatattactgtcaagagaggggacc
Phalaenopsis_ze tacaacatatattactgtcaagagaggggacc
Phalaenopsis_ma tacaacatatattactgtcaagagaggggacc
Phalaenopsis_te tacaacatatattactgtcaagagaggggacc
Phalaenopsis_co tacaacatatattactgtcaagagaggggacc
Phalaenopsis_hi tacaacatatattactgtcaagagaggggacc
Phalaenopsis_lu tacaacatatattactgtcaagagaggggacc
Phalaenopsis_re tacaacatatattactgtcaagagaggggacc
Phalaenopsis_pa tacaacatatattactgtcaagagaggggacc
Phalaenopsis_fa tacaacatatattactgtcaagagaggggacc
Phalaenopsis_pu tacaacatatattactgtcaagagaggggacc
Phalaenopsis_mo tacaacatatattactgtcaagagaggggacc
Phalaenopsis_fi tacaacatatattactgtcaagagaggggacc
Be careful if there are blue Phalaenopsis_vi tacaacatatattactgtcaagagaggggacc
lines. 
By default, MAFFT Phalaenopsis_be tacaacatatattactgtcaagagaggggacc
considers similarities in Phalaenopsis_fl tacaacatatattactgtcaagagaggggacc
forward strands (red) only, but Phalaenopsis_pa tacaacatagattactgtcaagagaggggacc
ignores similarities in reverse Phalaenopsis_bo tacaacatagattactgtcaagagaggggacc
strands (blue). 
If blue lines are Phalaenopsis_co tacaacatagattactgtcaagaggggggacc
Phalaenopsis_la tacaacatagattactgtcaagagaggggacc
seen around diagonal regions Phalaenopsis_mi tacaacatagattactgtcaagagaggggacc
in the plots above, try the Phalaenopsis_am tacaacatatattactgtcaagagaggggacc
“Adjust direction” option in the Phalaenopsis_ve tacaacatatattactgtcaagagaggggacc
input page. Phalaenopsis_ba tacaacatatattactgtcaagagaggggacc
Phalaenopsis_am tacaacatatattactgtcaagagaggggacc
The above plots are based on Phalaenopsis_sa tacaacatatattactgtcaagagaggggacc
the original input sequences. 
Phalaenopsis_ap tacaacatatattactgtcaagagaggggacc
Phalaenopsis_ce tacaacatatattactgtcaagagaggggacc
Replot
the output sequences Phalaenopsis_sc tacaacatatattactgtcaagagaggggacc
(renumbered).  Phalaenopsis_ph tacaacatatattactgtcaagagaggggacc
Phalaenopsis_st tacaacatatattactgtcaagagaggggacc
Also note that MAFFT does not Phalaenopsis_eq tacaacatatattactgtcaagagaggggacc
assume genomic Phalaenopsis_lo tacaacatatattactgtcaagagaggggacc
Phalaenopsis_br tacaacatatattactgtcaagagaggggacc
rearrangements. Phalaenopsis_wi tacaacatatattactgtcaagagaggggacc
Phalaenopsis_de tacaacatatattactgtcaagagaggggacc
Phalaenopsis_ap tacaacatatattactgtcaagagaggggacc
Phalaenopsis_lo tacaacatatattactgtcaagagaggggacc
Phalaenopsis_pa tacaacatatattactgtcaagagaggggacc
Phalaenopsis_ma tacaacatatattactgtcaagagaggggacc
Phalaenopsis_gi tacaacatatattactgtcaagagaggggacc
Phalaenopsis_vi tacaacatatattactgtcaagagaggggacc
Phalaenopsis_co tacaacatatattactgtcaagagaggggacc
Phalaenopsis ku tacaacatatattactgtcaagagaggggacc
https://mafft.cbrc.jp/alignment/server/spool/_ho.220521162810002BiGaA3NhfqUjpYOr6Fm8vlsfnormal.html 1/1