build.md

Goalign: toolkit and api for alignment manipulation

Commands

build

This command builds bootstrap replicates from an input alignment (fasta or phylip) on different ways with different sub-commands:

1. goalign build seqboot : Builds bootstrap alignments from an input alignment (nt or aa). Sequence order may be shuffled with option -S. Output alignments may be written in compressed files (--gz) and/or added in a tar archive (--tar).
2. goalign build distboot: Builds bootstrap distance matrices based on different models, from an input alignment (nt only). It builds n bootstrap alignments and computes a distance matrix for each replicate. All distance matrices are written in the output file. If the input alignment file contains several alignments, it will take the first one only. The following models for distance computation are available:
   • pdist
   • jc : Juke-Cantor
   • k2p : Kimura 2 Parameters
   • f81 : Felsenstein 81
   • f84 : Felsenstein 84
   • tn93 : Tamura and Nei 1993

Usage

• General command

Usage:
  goalign build [command]

Available Commands:
  distboot    Builds bootstrap distances matrices
  seqboot     Builds bootstrap alignments

Flags:
  -h, --help   help for build

Global Flags:
  -i, --align string   Alignment input file (default "stdin")
  -p, --phylip         Alignment is in phylip? default=Fasta
  -t, --threads int    Number of threads (default 1)
  --input-strict       Strict phylip input format (only used with -p)
  --output-strict      Strict phylip output format  (only used with -p)

• distboot command

Usage:
  goalign build distboot [flags]

Flags:
  -m, --model string    Model for distance computation (default "k2p")
  -n, --nboot int       Number of bootstrap replicates to build (default 1)
  -o, --output string   Distance matrices output file (default "stdout")
  -r, --rm-gaps         Do not take into account positions containing >=1 gaps
      --seed int        Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1)

Global Flags:
  -i, --align string   Alignment input file (default "stdin")
  -p, --phylip         Alignment is in phylip? False=Fasta
  -t, --threads int    Number of threads (default 1)
  --input-strict       Strict phylip input format (only used with -p)
  --output-strict      Strict phylip output format  (only used with -p)

• seqboot command

Usage:
  goalign build seqboot [flags]

Flags:
      --gz                  Will gzip output file(s). Maybe slow if combined with --tar (only one thread working for tar/gz)
  -n, --nboot int           Number of bootstrap replicates to build (default 1)
  -o, --out-prefix string   Prefix of output bootstrap files (default "none")
      --seed int            Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1)
  -S, --shuf-order          Also shuffle order of sequences in bootstrap files
      --tar                 Will create a single tar file with all bootstrap alignments (one thread for tar, but not a bottleneck)

Global Flags:
  -i, --align string   Alignment input file (default "stdin")
  -p, --phylip         Alignment is in phylip? False=Fasta
  -t, --threads int    Number of threads (default 1)
  --input-strict       Strict phylip input format (only used with -p)
  --output-strict      Strict phylip output format  (only used with -p)

Examples

• Generate a random tree with 100 leaves (Gotree), then simulate an alignment with 500 sites (seq-gen), compute 100 bootstrap distance matrices with Goalign (f81 model and 10 threads), infer trees for all bootstrap distance matrices and for simulated alignment (FastME), and compute bootstrap supports (Gotree):

gotree generate yuletree -l 100 --seed 1 -o true_tree.nw
seq-gen -op -mGTR -l500 -z 2 -n 1 true_tree.nw > alignment.phy
goalign build distboot -i alignment.phy -m f81 -n 100 -o dist_boot.txt -p -t 10
fastme -i dist_boot.txt -D 100 -o boot_trees.nw
fastme -i alignment.phy -d1 -o inferred_tree.nw
gotree compute support classical -i inferred_tree.nw -b boot_trees.nw -o inferred_tree_supports.nw -t 10

Should give the following tree with branches having > 70% support highlighted.

• Generate a random tree with 100 leaves (Gotree), then simulate an alignment with 500 sites (seq-gen), compute 100 bootstrap alignments Goalign (f81 model and 10 threads), infer trees for all bootstrap alignments and for the simulated alignment (FastTree), and compute bootstrap supports (Gotree):

gotree generate yuletree -l 100 --seed 1 -o true_tree.nw
seq-gen -op -mGTR -l500 -z 2 -n 1 true_tree.nw > alignment.phy
goalign build seqboot -i alignment.phy -p -n 100 -o seq_boot -S
cat seq_boot*.ph | FastTree -nt -n 100 -gtr > boot_trees.nw
FastTree -nt -gtr alignment.phy  > inferred_tree.nw
gotree compute support classical -i inferred_tree.nw -b boot_trees.nw -o inferred_tree_supports.nw -t 10

Should give the following tree with branches having > 70% support highlighted.