### Mx1 in bats

#### fragment_1

D | E | C | M | K
R | S | T | F | Y
N | Q | G | L | V
I | A | W | H | P

Input

- Fasta (nt)
- Fasta (aa)

Alignment

- nt:
  full, no gaps
- aa:
  full, no gaps

Tree

- nt:
  newick, pdf, svg
- aa:
  newick, pdf, svg

Codeml

- Go to overview

Recombination

- Model: 010010
- Tree topologies
- GARD

- full_aln
- fragment_2
- fragment_3

Significant sites

- no gaps:
  tex, pdf
- with gaps:
  tex, pdf

go back to full alignment

Parameters

PoSeiDon v1.1

|  | Fragment_1
|  | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106
|  | --- | --- | --- | --- | --- | --- | --- | ATG | GGT | GTC | CCT | CAA | GGG | AAA | ATC | CAA | AAC | CAT | GAT | TTG | GCC | TTT | GCA | GCC | AGT | CCT | CCG | TTA | CCA | AAT | ACT | GAG | GTG | --- | --- | TCT | GAG | AAG | AAT | CCG | GAA | AAA | AGG | GAA | GAG | AGC | AGC | CTA | TGC | AGC | CAC | TAC | GAG | GAG | AAG | GTC | CGC | CCC | TGC | ATC | GAC | CTC | ATC | GAC | TCC | CTG | CGG | GCC | CTG | GGC | GTG | GAG | CAG | GAC | CTG | GCC | CTG | CCC | GCC | ATT | GCG | GTC | ATC | GGG | GAC | CAG | AGC | TCG | GGC | AAG | AGC | TCC | GTG | CTG | GAG | GCC | CTG | TCC | GGC | GTC | GCC | CTC | CCC | AGG | GGC | AGC
| --- | --- | --- | --- | --- | --- | --- | ATG | GGT | GTT | CCT | CAA | GTG | AAA | GTC | GAA | AGT | CAT | GGC | TCG | GCC | TCT | GCA | CCC | ATT | CCT | CAG | TTA | CCA | AAT | GCT | GAG | GTG | --- | --- | CCT | GAG | AAG | AAT | CTG | GAC | AAA | GGG | GAC | GAG | ATA | AAC | CTG | TGC | AGC | TAC | TAC | GAG | GAG | AAG | GTC | CGC | CCC | TGC | ATC | GAC | CTC | ATC | GAC | TCT | CTG | CGG | GCC | CTG | GGC | GTG | GAG | CAG | GAC | CTG | GCC | CTG | CCC | GCC | ATC | GCG | GTC | ATC | GGG | GAC | CAG | AGC | TCG | GGC | AAG | AGC | TCC | GTG | CTG | GAG | GCC | CTG | TCG | GGC | GTC | GCC | CTC | CCC | AGA | GGC | AGC
| --- | --- | --- | --- | --- | --- | --- | ATG | GGT | GTT | CCT | CAA | GTG | AAA | GTC | CAA | GGT | CAT | AGC | TCG | GAC | CTT | GCA | TCC | GCG | CCT | CAG | TTA | CCA | AAT | GCT | GAG | GTG | --- | --- | CCT | GAG | AAG | AAT | CTA | AAA | AAA | GGG | GAA | GAG | ACA | GAC | CTG | TGC | AGC | CAC | TAC | GAG | GAG | AAG | GTC | CGC | CCC | TGC | ATC | GAC | CTC | GTC | GAC | TCT | CTG | CGG | GCC | CTG | GGC | GTG | GAG | CAG | GAC | CTG | GCC | CTG | CCC | GCC | ATC | GCG | GTC | ATC | GGG | GAC | CAG | AGC | TCG | GGC | AAG | AGC | TCG | GTG | CTG | GAG | GCC | CTG | TCG | GGC | GTT | GCC | CTC | CCC | AGA | GGC | AGC
| ATG | AAT | CCT | CCT | ACA | GTG | AAG | AGG | AGT | CCT | CTT | AAA | GTG | AAA | GTC | AAA | AAT | CAT | AAT | TCG | GCC | TCT | GCG | TCC | AGT | CCT | CGG | TTA | CCA | GAT | GCT | AAG | GTG | --- | --- | TCT | GAG | GAG | AAT | CTG | GAA | AAA | GGC | ACC | GAG | AGC | AGC | CTG | TGC | AGC | TAC | TAC | GAG | GAG | AAA | ATC | CGC | CCC | TGC | ATC | GAC | CTC | ATC | GAC | TCT | CTG | CGG | GCC | CTG | GGC | GTG | GAG | CAG | GAC | CTG | GCC | CTG | CCC | GCC | ATC | GCG | GTC | ATC | GGG | GAC | CAG | AGC | TCG | GGC | AAG | AGC | TCC | GTG | CTG | GAG | GCC | CTG | TCG | GGC | GTC | GCC | CTG | CCC | AGA | GGC | AGC
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ATG | GAA | ACA | GCA | AGT | CCT | GAT | TCC | ACC | CCT | GCA | CCC | AGT | CAT | CCC | TTA | CCA | AAT | GGA | GAT | GCT | GTT | ACG | CCG | GAG | GGA | AAT | CTG | GAG | ACG | ACG | TTG | GAG | AAT | AGC | CTG | TGC | AGC | CAG | TAC | GAG | GAG | AAG | GTG | CGC | CCC | TGC | ATC | GAC | CTC | ATC | GAC | TCC | CTG | CGG | GCC | CTG | GGC | GTG | GAG | CAG | GAC | CTG | GCC | CTG | CCC | GCC | ATC | GCC | GTC | ATC | GGG | GAC | CAG | AGC | TCG | GGA | AAG | AGC | TCC | GTG | CTG | GAG | GCG | CTG | TCT | GGT | GTC | TCC | CTC | CCC | AGA | GGC | AGC
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ATG | GAA | ACA | GCA | ACT | CCT | GAC | TCC | ACC | CTT | GCA | TCC | AGT | CAT | CCC | TTA | CCA | AAT | GGA | GAT | GCT | GTT | ACG | CCG | GAG | GGA | AAT | CTG | GAG | ACA | ACG | TTG | GAG | AAT | AGC | CTG | TGC | AGC | CAG | TAC | GAG | GAG | AAG | GTG | CGC | CCC | TGC | ATC | GAC | CTC | ATC | GAC | TCC | CTG | CGG | GCC | CTG | GGC | GTG | GAG | CAG | GAC | CTG | GCC | CTG | CCC | GCC | ATC | GCC | GTC | ATC | GGG | GAC | CAG | AGC | TCG | GGC | AAG | AGC | TCC | GTG | CTG | GAG | GCG | CTG | TCT | GGT | GTC | TCC | CTC | CCC | AGA | GGC | AGC
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ATG | GAA | ACG | GCA | ACT | CCC | GAC | TCC | ACC | TCC | GCG | TCT | GGC | CAG | CCC | TTA | CCC | AAT | GGA | GAT | GCT | GTT | GGG | CCA | GAG | GTA | AAT | CCG | GAG | GCA | ATG | CTG | GAG | ACG | AGC | TTG | TGC | AGC | CAG | TAC | GAG | GAG | AAG | GTG | CGC | CCC | TGC | ATC | GAC | CTC | ATC | GAC | TCC | CTG | CGG | GCC | CTG | GGC | GTG | GAG | CAG | GAC | CTG | GCC | CTG | CCC | GCC | ATC | GCC | GTC | ATC | GGG | GAC | CAG | AGC | TCG | GGC | AAG | AGC | TCA | GTG | CTG | GAG | GCG | CTG | TCT | GGT | GTC | TCC | CTC | CCC | AGA | GGC | AGC
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ATG | GAG | ACA | GCG | ACT | CCC | GAC | TCC | GCC | TCT | GCA | TCC | AGT | CAG | CCC | TTA | CCC | AAT | GGA | GAT | GCT | GTG | GTG | CCA | GAA | GTA | AAC | ATG | GAG | ACA | ATG | CTG | GAG | ACC | AGC | CTG | TGC | AGC | CAG | TAC | GAG | GAG | AAG | GTG | CGG | CCC | TGC | ATC | GAC | CTC | ATC | GAC | TCC | CTG | CGG | GCC | CTG | GGC | GTG | GAG | CAG | GAC | CTG | GCC | CTG | CCC | GCC | ATC | GCC | GTC | ATC | GGG | GAC | CAG | AGC | TCG | GGC | AAG | AGC | TCC | GTG | CTG | GAG | GCG | CTG | TCG | GGT | GTC | GCC | CTC | CCC | AGA | GGC | AGC
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ATG | GAA | ACA | GCA | ACT | CCT | GAT | TCC | ACC | CCT | GCA | TCC | AGT | CAT | CCC | TTA | CCA | AAT | GGA | GAT | GCT | GTT | GAG | CCG | GAG | GGA | AAT | CTG | GAG | ACA | ACG | TTG | GAG | AAT | AGC | CTG | TGC | AGC | CAG | TAC | GAG | GAG | AAG | GTG | CGC | CCC | TGC | ATC | GAC | CTC | ATT | GAC | TCC | CTG | CGG | GCC | CTG | GGT | GTG | GAG | CAG | GAC | CTG | GCC | CTG | CCT | GCC | ATC | GCC | GTC | ATC | GGG | GAC | CAG | AGC | TCG | GGC | AAG | AGC | TCC | GTG | CTG | GAG | GCG | CTG | TCT | GGT | GTC | TCC | CTC | CCC | AGA | GGC | AGC
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ATG | GAA | ACA | GCA | ACT | CCT | GAT | TCC | ACC | CCT | GCA | TCC | AGT | CAT | CCC | TTA | CCA | AAT | GGA | GAT | GCT | GTT | GCG | CCG | GAG | GGA | AAT | CTG | GAG | ACA | ACG | TTG | GAG | AAT | AGC | CTG | TGC | AGC | CAG | TAC | GAG | GAG | AAG | GTG | CGC | CCC | TGC | ATC | GAC | CTC | ATC | GAC | TCC | CTG | CGG | GCC | CTG | GGC | GTG | GAG | CAG | GAC | CTG | GCC | CTG | CCC | GCC | ATC | GCC | GTC | ATC | GGG | GAC | CAG | AGC | TCG | GGC | AAG | AGC | TCC | GTG | CTG | GAG | GCG | CTG | TCT | GGT | GTC | TCC | CTC | CCC | AGA | GGC | AGC
| --- | --- | --- | --- | --- | --- | --- | ATG | GTT | CAT | TCT | GAC | CTG | CAA | ACC | GAA | AAT | CCC | AGT | TCG | GCC | TCT | ACA | TCC | AAT | GAT | GAG | CTA | CCA | AAT | ACA | AAT | GCT | GAT | AGG | CCT | GAG | AAA | AAT | CTG | GCC | ACG | AAG | CTG | GAG | CAC | CAC | CTG | TGC | AGC | CAC | TAC | GAG | GAG | AAG | GTG | CGC | CCC | TGC | ATT | GAC | CTC | ATC | GAC | TCC | CTG | CGG | GCC | CTG | GGC | GTG | GAG | CAG | GAC | CTG | GCC | CTG | CCC | GCC | ATC | GCC | GTC | ATC | GGG | GAC | CAG | AGC | TCG | GGC | AAG | AGC | TCC | GTG | CTG | GAG | GCC | CTG | TCG | GGC | GTC | GCC | CTC | CCC | AGA | GGC | AGC
| --- | --- | --- | --- | --- | --- | --- | ATG | GTT | CGT | TCT | GGC | CTG | CAA | ACC | AGA | AAT | CCC | AAT | TCT | --- | TCT | ACA | TCC | AAT | CGT | GAA | CAA | TCA | AAT | GAA | AAT | GCT | GAT | GAG | CCA | AAG | AAA | AAT | CGG | GAC | ACA | --- | CTC | GAG | CAC | CAC | CTG | TGC | AGC | CAG | TAT | GAG | GAG | AAG | GTG | CGT | CCC | TGC | ATC | GAC | CTC | GTG | GAC | TCC | CTG | CGG | GCC | CTG | GGC | GTG | GAG | CAG | GAC | CTG | GCC | CTG | CCC | GCC | ATC | GCC | GTC | ATC | GGG | GAC | CAG | AGC | TCA | GGC | AAG | AGC | TCC | GTG | CTG | GAG | GCC | CTG | TCG | GGT | GTC | GCC | CTC | CCC | AGA | GGC | AGT
| --- | --- | --- | --- | --- | --- | --- | ATG | GTT | CGT | TCT | GGC | CTG | CAA | ACG | GAA | AAT | CCC | AAT | TCG | GCT | TCT | GTA | TCC | AAT | CAT | GAA | CAA | TCA | AAT | GAA | AAT | GCT | GAT | AAG | CCA | AAG | AAA | AAT | GTG | GAC | ACA | GAG | CTC | GAG | CAC | CGC | CTG | TGC | AGC | CAG | TAC | GAG | GAG | AAG | GTG | CGC | CCC | TGC | ATC | GAC | CTC | GTG | GAC | TCC | CTG | CGG | GCC | CTG | GGC | GTG | GAG | CAG | GAC | CTG | GCC | CTG | CCC | GCC | ATC | GCC | GTC | ATC | GGG | GAC | CAG | AGC | TCG | GGC | AAG | AGC | TCC | GTG | CTG | GAG | GCC | CTG | TCG | GGC | GTC | GCC | CTC | CCC | AGA | GGC | AGC
| F3X4, M1a vs M2a | LRT is significant lnL_M1a = -1181.57 lnL_M2a = -1172.75 LRT: χ2 = 17.64 % sites with ω > 1 = 18.19 avg(ω) = 2.96 p < 0.001 |  |  |  |  |  |  |  |  |  |  |  |  |  | 0.529 |  | 0.989 | 0.892 |  | 0.895 |  |  | 0.994 | 0.847 |  | 0.977 | 0.919 | 0.844 | 0.531 |  |  | 0.954 | 0.578 |  |  |  | 0.649 |  | 0.791 |  | 0.910 | 0.618 | 0.618 |  | 0.979 |  | 0.874 | 0.597 |  |  |  | 0.643 |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
| F3X4, M7/M8a vs M8 | LRT is significant lnL_M7 = -1184.87 / lnL_M8a = -1182.19 lnL_M8 = -1172.84 LRT: χ2 = 24.05 / LRT: χ2 = 18.7 % sites with ω > 1 = 21.3 avg(ω) = 2.76 p < 0.001 / p < 0.001 |  |  |  |  |  |  |  |  |  |  |  |  | 0.582 | 0.761 |  | 0.999 | 0.982 |  | 0.986 |  |  | 0.999 | 0.966 | 0.623 | 0.997 | 0.987 | 0.975 | 0.663 |  |  | 0.993 | 0.859 |  |  |  | 0.853 |  | 0.961 |  | 0.988 | 0.901 | 0.834 |  | 0.998 |  | 0.981 | 0.910 |  |  |  | 0.920 |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
| F1X4, M1a vs M2a | LRT is significant lnL_M1a = -1187.64 lnL_M2a = -1179.83 LRT: χ2 = 15.62 % sites with ω > 1 = 28.34 avg(ω) = 2.2 p < 0.001 |  |  |  |  |  |  |  |  |  |  |  |  | 0.627 | 0.537 | 0.584 | 0.982 | 0.917 |  | 0.946 |  |  | 0.989 | 0.811 | 0.635 | 0.972 | 0.905 | 0.898 |  |  |  | 0.937 | 0.745 |  |  |  | 0.637 |  | 0.867 |  | 0.934 | 0.818 | 0.590 |  | 0.989 |  | 0.957 | 0.880 |  |  |  | 0.814 |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
| F1X4, M7/M8a vs M8 | LRT is significant lnL_M7 = -1190.02 / lnL_M8a = -1187.65 lnL_M8 = -1179.85 LRT: χ2 = 20.33 / LRT: χ2 = 15.61 % sites with ω > 1 = 31.04 avg(ω) = 2.12 p < 0.001 / p < 0.001 |  |  |  |  |  |  |  |  |  |  |  |  | 0.808 | 0.645 | 0.734 | 0.998 | 0.983 |  | 0.991 |  |  | 0.999 | 0.935 | 0.815 | 0.996 | 0.980 | 0.978 | 0.518 |  |  | 0.987 | 0.900 |  |  |  | 0.761 |  | 0.969 |  | 0.989 | 0.952 | 0.709 |  | 0.999 |  | 0.993 | 0.976 |  |  |  | 0.952 |  |  |  |  |  |  |  |  |  |  |  | 0.595 |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
| F61, M1a vs M2a | LRT is significant lnL_M1a = -1195.67 lnL_M2a = -1186.04 LRT: χ2 = 19.27 % sites with ω > 1 = 30.62 avg(ω) = 2.34 p < 0.001 |  |  |  |  |  |  |  |  |  |  |  |  | 0.726 | 0.521 | 0.693 | 0.983 | 0.858 |  | 0.940 |  |  | 0.982 | 0.784 | 0.793 | 0.956 | 0.875 | 0.950 |  |  |  | 0.926 | 0.714 |  |  |  | 0.551 |  | 0.879 |  | 0.977 | 0.893 | 0.551 |  | 0.996 |  | 0.976 | 0.943 |  |  |  | 0.901 |  |  |  |  |  |  |  |  |  |  |  | 0.634 |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 0.580 |  |  |  |  |
| F61, M7/M8a vs M8 | LRT is significant lnL_M7 = -1197.14 / lnL_M8a = -1195.68 lnL_M8 = -1188.64 LRT: χ2 = 17.01 / LRT: χ2 = 14.08 % sites with ω > 1 = 38.07 avg(ω) = 1.92 p < 0.001 / p < 0.001 |  |  |  |  |  |  |  |  |  |  |  |  | 0.873 | 0.606 | 0.804 | 0.997 | 0.959 |  | 0.988 |  |  | 0.997 | 0.910 | 0.915 | 0.991 | 0.965 | 0.989 |  |  |  | 0.982 | 0.863 |  |  |  | 0.646 |  | 0.967 |  | 0.996 | 0.972 | 0.645 |  | 0.999 |  | 0.996 | 0.988 |  |  |  | 0.974 |  |  |  |  |  |  |  |  |  |  |  | 0.758 |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 0.680 |  |  |  |  |
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| - | - | - | - | - | - | - | M | V | H | S | D | L | Q | T | E | N | P | S | S | A | S | T | S | N | D | E | L | P | N | T | N | A | D | R | P | E | K | N | L | A | T | K | L | E | H | H | L | C | S | H | Y | E | E | K | V | R | P | C | I | D | L | I | D | S | L | R | A | L | G | V | E | Q | D | L | A | L | P | A | I | A | V | I | G | D | Q | S | S | G | K | S | S | V | L | E | A | L | S | G | V | A | L | P | R | G | S |
| - | - | - | - | - | - | - | M | V | R | S | G | L | Q | T | R | N | P | N | S | - | S | T | S | N | R | E | Q | S | N | E | N | A | D | E | P | K | K | N | R | D | T | - | L | E | H | H | L | C | S | Q | Y | E | E | K | V | R | P | C | I | D | L | V | D | S | L | R | A | L | G | V | E | Q | D | L | A | L | P | A | I | A | V | I | G | D | Q | S | S | G | K | S | S | V | L | E | A | L | S | G | V | A | L | P | R | G | S |
| - | - | - | - | - | - | - | M | V | R | S | G | L | Q | T | E | N | P | N | S | A | S | V | S | N | H | E | Q | S | N | E | N | A | D | K | P | K | K | N | V | D | T | E | L | E | H | R | L | C | S | Q | Y | E | E | K | V | R | P | C | I | D | L | V | D | S | L | R | A | L | G | V | E | Q | D | L | A | L | P | A | I | A | V | I | G | D | Q | S | S | G | K | S | S | V | L | E | A | L | S | G | V | A | L | P | R | G | S |
| M | N | P | P | T | V | K | R | S | P | L | K | V | K | V | K | N | H | N | S | A | S | A | S | S | P | R | L | P | D | A | K | V | - | - | S | E | E | N | L | E | K | G | T | E | S | S | L | C | S | Y | Y | E | E | K | I | R | P | C | I | D | L | I | D | S | L | R | A | L | G | V | E | Q | D | L | A | L | P | A | I | A | V | I | G | D | Q | S | S | G | K | S | S | V | L | E | A | L | S | G | V | A | L | P | R | G | S |
| - | - | - | - | - | - | - | M | G | V | P | Q | G | K | I | Q | N | H | D | L | A | F | A | A | S | P | P | L | P | N | T | E | V | - | - | S | E | K | N | P | E | K | R | E | E | S | S | L | C | S | H | Y | E | E | K | V | R | P | C | I | D | L | I | D | S | L | R | A | L | G | V | E | Q | D | L | A | L | P | A | I | A | V | I | G | D | Q | S | S | G | K | S | S | V | L | E | A | L | S | G | V | A | L | P | R | G | S |
| - | - | - | - | - | - | - | M | G | V | P | Q | V | K | V | E | S | H | G | S | A | S | A | P | I | P | Q | L | P | N | A | E | V | - | - | P | E | K | N | L | D | K | G | D | E | I | N | L | C | S | Y | Y | E | E | K | V | R | P | C | I | D | L | I | D | S | L | R | A | L | G | V | E | Q | D | L | A | L | P | A | I | A | V | I | G | D | Q | S | S | G | K | S | S | V | L | E | A | L | S | G | V | A | L | P | R | G | S |
| - | - | - | - | - | - | - | M | G | V | P | Q | V | K | V | Q | G | H | S | S | D | L | A | S | A | P | Q | L | P | N | A | E | V | - | - | P | E | K | N | L | K | K | G | E | E | T | D | L | C | S | H | Y | E | E | K | V | R | P | C | I | D | L | V | D | S | L | R | A | L | G | V | E | Q | D | L | A | L | P | A | I | A | V | I | G | D | Q | S | S | G | K | S | S | V | L | E | A | L | S | G | V | A | L | P | R | G | S |