Documentation ¶
Index ¶
Constants ¶
This section is empty.
Variables ¶
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var RootCmd = &cobra.Command{ Use: "goalign", Short: "goalign: A set of tools to handle sequence alignments", Long: `goalign: A set of tools to handle sequence alignments. It allows to : 1 - Convert formats 2 - Shuffle alignments 3 - Sample alignments 4 - Print informations about alignments 5 - Generate bootstrap alignments Input alignment file formats: 1. Fasta (default) 2. Phylip (-p option) 3. Nexus (-x option) 4. Auto detect (--auto-detect option). In that case, it will test input formats in the following order: 1. Fasta 2. Nexus 3. Phylip If none of these formats is recognized, then will exit with an error Please note that in --auto-detect mode, phylip format is considered as not strict! `, PersistentPreRun: func(cmd *cobra.Command, args []string) { runtime.GOMAXPROCS(rootcpus) rootaligns = readalign(infile) }, PersistentPostRun: func(cmd *cobra.Command, args []string) { if rootaligns.Err != nil { io.ExitWithMessage(rootaligns.Err) } }, }
RootCmd represents the base command when called without any subcommands
View Source
var Version string = "Unset"
Functions ¶
Types ¶
This section is empty.
Source Files ¶
- addgaps.go
- addid.go
- alleles.go
- bootstrap.go
- build.go
- char.go
- clean.go
- cleanseqs.go
- cleansites.go
- compute.go
- computedist.go
- computeentropy.go
- concat.go
- distboot.go
- divide.go
- draw.go
- draw_biojs.go
- fasta.go
- gaps.go
- length.go
- mutate.go
- nalign.go
- name.go
- nexus.go
- nseq.go
- paml.go
- phylip.go
- pssm.go
- random.go
- rarefy.go
- recomb.go
- reformat.go
- rename.go
- rogue.go
- root.go
- sample.go
- sampleseq.go
- samplesites.go
- seq.go
- seqs.go
- shuffle.go
- sites.go
- sort.go
- stats.go
- subseq.go
- subset.go
- swap.go
- taxa.go
- tnt.go
- trim.go
- unalign.go
- version.go
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