Alignment recoding

Recode alignment into reduced alphabets

Command identity

Canonical command:

alignment_recoding

Handler:

alignment_recoding

Aliases:

aln_recoding, recode

Standalone executables:

pk_alignment_recoding, pk_aln_recoding, pk_recode

Categories:

Alignment & dataset utilities

Runtime interface

Synopsis

phykit alignment_recoding <alignment> [--code <code>] [--json]

Arguments

This table is generated from the live command parser. It is the authoritative source for accepted spellings, required arguments, types, defaults, and choices.

Argument	Required	Type	Default	Choices
alignment	true	str	required	any
-c, --code	false	str	none	any
--json	false	boolean	false	any

Output and errors

--json provides the command's structured JSON representation. Unless the guidance below states otherwise, results are emitted as command output. Invalid command syntax exits with status 2. Input validation and scientific limitations are described in the guidance below.

Guidance, interpretation, and examples

Recode alignments using reduced character states.

Alignments can be recoded using established or custom recoding schemes. Recoding schemes are specified using the -c/--code argument. Custom recoding schemes can be used and should be formatted as a two column file wherein the first column is the recoded character and the second column is the character in the alignment.

phykit alignment_recoding <fasta> [-c/--code <code>] [--json]

Codes for which recoding scheme to use:
RY-nucleotide
R = purines (i.e., A and G)
Y = pyrimidines (i.e., T and C)

SandR-6
0 = A, P, S, and T
1 = D, E, N, and G
2 = Q, K, and R
3 = M, I, V, and L
4 = W and C
5 = F, Y, and H

KGB-6
0 = A, G, P, and S
1 = D, E, N, Q, H, K, R, and T
2 = M, I, and L
3 = W
4 = F and Y
5 = C and V

Dayhoff-6
0 = A, G, P, S, and T
1 = D, E, N, and Q
2 = H, K, and R
3 = I, L, M, and V
4 = F, W, and Y
5 = C

Dayhoff-9
0 = D, E, H, N, and Q
1 = I, L, M, and V
2 = F and Y
3 = A, S, and T
4 = K and R
5 = G
6 = P
7 = C
8 = W

Dayhoff-12
0 = D, E, and Q
1 = M, L, I, and V
2 = F and Y
3 = K, H, and R
4 = G
5 = A
6 = P
7 = S
8 = T
9 = N
A = W
B = C

Dayhoff-15
0 = D, E, and Q
1 = M and L
2 = I and V
3 = F and Y
4 = G
5 = A
6 = P
7 = S
8 = T
9 = N
A = K
B = H
C = R
D = W
E = C

Dayhoff-18
0 = F and Y
1 = M and L
2 = I
3 = V
4 = G
5 = A
6 = P
7 = S
8 = T
9 = D
A = E
B = Q
C = N
D = K
E = H
F = R
G = W
H = C

Options:
<alignment>: first argument after function name should be an alignment file
-c/--code: argument to specify the recoding scheme to use
--json: optional argument to print results as JSON