Man pages for olli0601/big.phylo
big.phylo
| cmd.examl.bootstrap | Generate the ExaML boostrap shell command, one bootstrap per... |
| cmd.examl.bootstrap.on.one.machine | Produce the ExaML boostrap shell command, all boostraps on a... |
| cmd.examl.bsalignment | Produce the shell command that creates the bootstrap... |
| cmd.examl.bsstarttree | Produce a shell command to compute the final boostrap tree. |
| cmd.examl.cleanup | Procude a shell command to clean up after an ExaML run. |
| cmd.examl.single | Produce a single ExaML shell command. |
| cmd.fasttree | Produce a single FastTree shell command. |
| cmd.fasttree.add.bootstrap.nodelabels.to.base.tree | Produce a single FastTree shell command on a bootstrap... |
| cmd.fasttree.many.bootstraps | Produce a single FastTree shell command on a bootstrap... |
| cmd.fasttree.one.bootstrap | Produce a single FastTree shell command on a bootstrap... |
| cmd.jmodeltest | Produce a single LSD shell command. |
| cmd.lsd | Produce a single LSD shell command. |
| cmd.lsd.dates | Generate the LSD Dates file. |
| cmd.multi2di | Produce a shell command to convert multi-furcating trees to... |
| cmd.mvr | Produce a single shell command to run MVR. |
| cmd.phydstar | Produce a single PhyD* shell command. |
| cmd.raxml | Produce a single RAxML shell command. |
| cmd.rm.resistance | Produce the shell command that masks resistance mutations. |
| cmd.strip.gaps | Procude a shell command to strip gaps from alignment. |
| cmd.treedater | Generate commands to date trees with TreeDater. |
| pipeline.ExaML.bootstrap.per.proc | Compute phylogeny with bootstrap values |
| prog.examl.getbootstrapseq | Program to generate a booststrap alignment |
| seq.align.based.on.common.reference | Merge two alignments with common reference |
| seq.blast | Perform online BLAST search |
| seq.blast.read | Read BLAST output |
| seq.dist | Compute pairwise distance matrix |
| seq.find | Find the row numbers in a sequence matrix with a particular... |
| seq.gc.content | Compute the GC content |
| seq.length | Compute the length of sequences |
| seq.proportion.ambiguous | Compute the proportion of ambiguous nucleotides |
| seq.read.GenBank | Read sequences from GenBank |
| seq.replace | Replace nucleotide codes in sequence alignment |
| seq.rm.drugresistance | Remove drug resistance mutations |
| seq.rmgaps | Remove gaps in sequence alignment |
| seq.strip.gap | Strip gaps |
| seq.unique | Compute a subset of unique sequences |
| seq.write.dna.nexus | Write a NEXUS file |
| seq.write.dna.phylip | Write a square phylip file |
| seq.write.dna.phylip.triangular | Write a triangular phylip file |
