Number of clades resolved
2
1.5
1
0.5
0
36
35
34
33
32
31
30
29
28
27
26
25
24
23
22
21
20
19
18
17
16
15
14
13
12
11
10
9
8
7
6
5
4
3
2
1
Parameter set
POY
MUSCLE
DCA
Fig. S1. Least squared means of the number of clades resolved by POY, MUSCLE, and DCA across the 36 alignment-parameter sets
when gaps were treated as missing data. Plus and minus one standard error is shown for each bar.
Number of clades resolved
2
1.5
1
0.5
0
36
35
34
33
32
31
30
29
28
27
26
25
24
23
22
21
20
19
18
17
16
15
14
13
12
11
10
9
8
7
6
5
4
3
2
1
Parameter set
POY
MUSCLE
DCA
Fig. S2. Least squared means of the number of clades resolved by POY, MUSCLE, and DCA across the 36 alignment-parameter sets
when gaps were coded using simple indel coding (SIC). Plus and minus one standard error is shown for each bar.
Number of clades resolved
2
1.5
1
0.5
0
36
35
34
33
32
31
30
29
28
27
26
25
24
23
22
21
20
19
18
17
16
15
14
13
12
11
10
9
8
7
6
5
4
3
2
1
Parameter set
POY
MUSCLE
DCA
Fig. S3. Least squared means of the number of clades resolved by POY, MUSCLE, and DCA across the 36 alignment-parameter sets
when gaps were coded as 5th states. Plus and minus one standard error is shown for each bar.
Number of clades resolved
2
1.5
1
0.5
0
36
35
34
33
32
31
30
29
28
27
26
25
24
23
22
21
20
19
18
17
16
15
14
13
12
11
10
9
8
7
6
5
4
3
2
1
Parameter set
POY
MUSCLE
DCA
Fig. S4. Least squared means of the number of clades resolved by POY, MUSCLE, and DCA across the 36 alignment-parameter sets
when characters were weighted using the “logically consistent” approach. Plus and minus one standard error is shown for each bar.
Averaged number of clades resolved
2
gaps = missing
1.5
POY
MUSCLE
DCA
1
0.5
0
36
35
34
33
32
31
30
29
28
27
26
25
24
23
22
21
20
19
18
17
16
15
14
13
12
11
10
9
8
7
6
5
4
3
2
1
Parameter set
Fig. S5. Least squared means of the averaged number of clades resolved by POY, MUSCLE, and DCA across the 36 alignmentparameter sets when gaps were treated as missing data. Plus and minus one standard error is shown for each bar.
Averaged number of clades resolved
2
gaps = SIC
1.5
POY
MUSCLE
DCA
1
0.5
0
36
35
34
33
32
31
30
29
28
27
26
25
24
23
22
21
20
19
18
17
16
15
14
13
12
11
10
9
8
7
6
5
4
3
2
1
Parameter set
Fig. S6. Least squared means of the averaged number of clades resolved by POY, MUSCLE, and DCA across the 36 alignmentparameter sets when gaps were coded using simple indel coding (SIC). Plus and minus one standard error is shown for each bar.
Averaged number of clades resolved
2
gaps = 5th state
1.5
POY
MUSCLE
DCA
1
0.5
0
36
35
34
33
32
31
30
29
28
27
26
25
24
23
22
21
20
19
18
17
16
15
14
13
12
11
10
9
8
7
6
5
4
3
2
1
Parameter set
Fig. S7. Least squared means of the averaged number of clades resolved by POY, MUSCLE, and DCA across the 36 alignmentparameter sets when gaps were coded as 5th states. Plus and minus one standard error is shown for each bar.
Averaged number of clades resolved
2
“logically consistent”
1.5
POY
MUSCLE
DCA
1
0.5
0
36
35
34
33
32
31
30
29
28
27
26
25
24
23
22
21
20
19
18
17
16
15
14
13
12
11
10
9
8
7
6
5
4
3
2
1
Parameter set
Fig. S8. Least squared means of the averaged number of clades resolved by POY, MUSCLE, and DCA across the 36 alignmentparameter sets when characters were weighted using the “logically consistent” approach. Plus and minus one standard error is shown
for each bar.