trouble reading output of clustal omega
I am using clustal omega provided by (( for performing MSA. I have given some sequences as input and got output as shown below.
CLUSTAL O(1.2.1) multiple sequence alignment
variant9 ------------------------------------------------------------
variant7 ------------------------------------------------------------
variant8 ----ECAB----------AAAAACAAAAGAAFAAAAE--CEEAAECBEA-ABAAFAABCC
variant5 -------------EAAAAAAAAAAAAAEGAAAACAA------------------------
variant6 -------------EAAAAAAAAAAAAAEGAAAACAA------------------------
variant2 -----------------EEAAAAAAA----------------------------------
variant1 EAEAABEAAAAAAEEABCAAAAAAACBAAAAAACCAAB----------------------
variant3 --FAHCDDAGHFHHHBFDDAAGAABCAAGDBFGCCDEHGBDHEAFCFFGGHGAHHABHCC
variant4 --FAHCDDAGHFHHHBFDDAAGAABCAAGDBFGCCDEHGADHEAFCFFGGHGAFHABHCC
variant10 --FAHCDDAGHFHHHBFDDAAGAABCAAGDBFGCCDEHGBDHEAFCFFGGHGAFHABHCC
variant9 ----EAAAAA----AAAAAAAAAABAAAAAAAAAAAAAAAAAAAABAAAAAAAAAACAAA
variant7 ----EAAAAA----AAAAAAAAEAEAAAAAAAAAAAAAAAAAAAABAAAAAAAAAACAAA
variant8 AACFBAFCACCAAFBECCABDABABGCAAFBAC--EBAFAGBBAAABAHDEECGBACAAE
variant5 --------------AA--AAACAAAAC----AC--CBABAB------AAAACACAACAAA
variant6 --------------AA--AAACAAAAC----AC--CBABAB------AAAACACAACAAA
variant2 --------AAAAAEAF--AAAAAAAAAAAAAA-------AAAAAABAAAAAAAAAACAAA
variant1 --------------AB--AAAAAAEACABCAEA--------------AAAABACAACAAA
variant3 CBFFEGFCDCACGEBF--GEDEDAEACCFCFFC--CGFFABAHFHHDHHAFGFCDACHGE
variant4 CBFFEGFCDCACGEAF--GEBEDAEACCFCFFC--CGFBABAHFHHDHHAFGFCDACHGE
variant10 CBFFEGFCDCACGEBF--GEBEDAEACCFCFFC--CGFBABAHFHHDHHAFGFCDACHGE
. * .. ** .
variant9 AAAAAAAAAAAAAAA---AAAAABAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAABA
variant7 AAAAAAAAAAAAAAA---AAAAABBAAAAAAAAAAAAAAAAAAAAAAAAAAAAEAAAAAA
variant8 --------------------AAACAAAEBEABBAB--AAGEFACGAEEAACGAABE----
variant5 AAAA--BACABBAAABEBADBAACAAAAAAAAAAAEAA--------EEEACAA------A
variant6 AAAA--BACABBAAABEBADBAACAAAAAAAAAAAEAA--------EEEACAA------A
variant2 AAAAAAAAAAAAAAA---AAAAABBAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAABAAA
variant1 BAAABABACAABGAA---A-AAACFAAAEAAAAAAEAAAA---------AAAA-------
variant3 ---EHDFCCDD---------------EBEB-DEEFGAHBB---------DEHE-------
variant4 ---EHDFCCDD---------------EBEB-DEEFEAAAA---------AABA-------
variant10 ---EHDFCCDD---------------EBEB-DEEFEAABA---------CCDA-------
variant9 AABAAAAAAAAAABAAAAAAAEAABACCDAAABCBFAAEEBAABABHBEABAGADFC-AC
variant7 AAAAAAAAAAAAAAAAAAAAAEAABACCDAABAABFAAEEBAABABHBEABAGADBC-AC
variant8 -EBBFAEABAAECAACAACA----BBCAB-----------------------------BE
variant5 EABAAAAAAAAACAADAAAA--------AAAAAAAECAAGAHBBDEHEGAGEGACFB-AA
variant6 EABAAAAAAAAACAADAAAA--------AAAAAAAECAAGAHBBDEHEGAGEGACFB-AA
variant2 AAAAAAAAAAAAAAAAAAAAAEAABACCDAABAABFAAEEBAABABHBEABAGADFC-AC
variant1 ---------AAACAAAAAAAAAAAAACABAA--------GAHBBDEHGGAGEGBCFB-AA
variant3 ---------GAGEGACFB--------------------------------AAGAAFFBEH
variant4 ---------AAAAAAAAAAAAAAA---------------------BBAAAAAAAAFAAAC
variant10 ---------AABCBFAAEEBAABA---------------------BHBEABAGADFC-AC
.*
variant9 AGADCECAAHAEEBF------------------
variant7 AGADCECACHAEEBF------------------
variant8 CAAEFACFHADAADAAAAEEHH-----------
variant5 GAAFFBEHHHHDCEFDGGBGHHEDHDDBHHHDF
variant6 GAAFFBEHHHGDDEFDGGBGHHEDHDDBHHHDF
variant2 AGADCECACHAEEBF------------------
variant1 GAAFFBEHHHGDCEFDGGBGHHEDHDHBHHHDF
variant3 --------HHGDCEFDGHBGHHEDHDDBHHHDF
variant4 CAAAAACCBAAACA-------------------
variant10 AGADCECCAHAEEBF------------------
I know that the '*' implies that all the matching characters but am confused in what the '.' implies. Are there any better methods than clustal omega for MSA?
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In MSA, a . represents a semi-conserved residue (* represents conserved residue).
This alignment does not look great. Were the starting sequences of similar length (and known to be related)? Just by eye it appears that there may be a couple of groups. Did you make a simple tree?