|
|
| Name |
Description |
Version |
Minimum Galaxy Version |
|
|
Maximum Likelihood Analysis |
3.3 |
16.01 |
|
|
MUSCLE: Multiple sequence alignment. Input can be fasta or phytab format. |
3.8 |
16.01 |
|
|
Converts TNT text output from Morphobank into UCSB-phylotable. |
1.0.0 |
16.01 |
|
|
aliscorecut :: Runs Aliscore then Alicut on an aligned sequence from phytab Muscle. |
1.0 |
16.01 |
|
|
Sub-sample trees from from a posterior distribution |
1.0.0 |
16.01 |
|
|
Calculates support for nodes of a single tree (bootstrap) using a file of multiple trees |
1.0.0 |
16.01 |
|
|
Removes gap in sequences |
1.0.1 |
16.01 |
|
|
Draw a Phylogenic Tree |
1.0 |
16.01 |
|
|
text from a dataset |
1.0.0 |
16.01 |
|
|
Estimate species tree with NJst from table of tree names and newick trees |
1.0.0 |
16.01 |
|
|
Phytab RaXML - RaXML for phytab format |
1 |
16.01 |
|
|
Converts interleaved fasta to non-interleaved |
1.0.0 |
16.01 |
|
|
prank: Multiple sequence alignment. Input can be fasta or phytab format. |
1.0.0 |
16.01 |
|
|
TagDust - A program to eliminate artifactual reads from next-generation sequencing data sets. |
1.13 |
16.01 |
|
|
Appends all input sequence files into one file |
1.0.0 |
16.01 |
|
|
Use RAxML to calculate SHtest to compare trees |
7.2.8 |
16.01 |
|
|
UCSB Hamster is a Galaxy port for the Hamster script which finds orthologs based on HMM's. |
1.0.0 |
16.01 |
|
|
Runs IlluQC Parallel verion |
1.0.0 |
16.01 |
|
|
Scythe - A very simple adapter trimmer. |
0.981 BETA |
16.01 |
|
|
Create pdf of phylogeny graphics from table of tree names and newick trees |
1.0.0 |
16.01 |
|
|
Runs Translate |
1.0.0 |
16.01 |
|
|
Runs EvolMAP. |
1.0.0 |
16.01 |
|
|
Modifies EvolMAP output |
1.0.0 |
16.01 |
|
|
Converts EvolMAP Output file to FASTA file |
1.0.0 |
16.01 |
|
|
Runs EvolMAP for longer (bigger) jobs. |
1.0.0 |
16.01 |
|
|
Modifies EvolMAP Output to exclude specific species. |
1.0.0 |
16.01 |
|
|
Convert Aligned FASTA to phylip Extended |
1.0.0 |
16.01 |
|
|
Run Phylomatic |
1.0.1 |
16.01 |
|
|
Convert Aligned FASTA to phylip Extended |
1.0.0 |
16.01 |
|
|
Pruning taxa from a tree or multiple trees |
1.0.0 |
16.01 |
|
|
Maximum Likelihood Analysis |
7.2.8 |
16.01 |
|
|
clearcut: Generate Neighbor Joining phylogeny. Input can be fasta or phytab format. |
1.0.0 |
16.01 |
|
|
LB_pruner: Identify genes on very long branches. |
1.0.0 |
16.01 |
|
|
Removes characters in a sequence |
1.0.0 |
16.01 |
|
|
Converts fasta file with sequences from same species and gene family to phytab format |
1.0.0 |
16.01 |
|
|
hmmsearch :: search profile(s) against a sequence database. Produces a phytab output. |
3.0 |
16.01 |
|
|
Selection of best-fit models of protein evolution. |
2.4 |
16.01 |
|
|
e.g. to get peptides from ESTs |
0.0.1 |
16.01 |
|
|
Runs phylobayes |
1.0.1 |
16.01 |
|
|
Phytab RaXML - RaXML for phytab format |
1 |
16.01 |
|
|
JModelTest description here. |
1.0 |
16.01 |
|
|
Assembly of transcriptomes. |
1.0.1 |
16.01 |
|
|
Maximum Likelihood Analysis |
3.3 |
16.01 |
|
|
MUSCLE: Multiple sequence alignment. Input can be fasta or phytab format. |
3.8 |
16.01 |
|
|
Converts TNT text output from Morphobank into UCSB-phylotable. |
1.0.0 |
16.01 |
|
|
aliscorecut :: Runs Aliscore then Alicut on an aligned sequence from phytab Muscle. |
1.0 |
16.01 |
|
|
Sub-sample trees from from a posterior distribution |
1.0.0 |
16.01 |
|
|
Calculates support for nodes of a single tree (bootstrap) using a file of multiple trees |
1.0.0 |
16.01 |
|
|
Removes gap in sequences |
1.0.1 |
16.01 |
|
|
Draw a Phylogenic Tree |
1.0 |
16.01 |
|
|
text from a dataset |
1.0.0 |
16.01 |
|
|
Estimate species tree with NJst from table of tree names and newick trees |
1.0.0 |
16.01 |
|
|
Phytab RaXML - RaXML for phytab format |
1 |
16.01 |
|
|
Converts interleaved fasta to non-interleaved |
1.0.0 |
16.01 |
|
|
prank: Multiple sequence alignment. Input can be fasta or phytab format. |
1.0.0 |
16.01 |
|
|
TagDust - A program to eliminate artifactual reads from next-generation sequencing data sets. |
1.13 |
16.01 |
|
|
Appends all input sequence files into one file |
1.0.0 |
16.01 |
|
|
Use RAxML to calculate SHtest to compare trees |
7.2.8 |
16.01 |
|
|
UCSB Hamster is a Galaxy port for the Hamster script which finds orthologs based on HMM's. |
1.0.0 |
16.01 |
|
|
Runs IlluQC Parallel verion |
1.0.0 |
16.01 |
|
|
Scythe - A very simple adapter trimmer. |
0.981 BETA |
16.01 |
|
|
Create pdf of phylogeny graphics from table of tree names and newick trees |
1.0.0 |
16.01 |
|
|
Runs Translate |
1.0.0 |
16.01 |
|
|
Runs EvolMAP. |
1.0.0 |
16.01 |
|
|
Modifies EvolMAP output |
1.0.0 |
16.01 |
|
|
Converts EvolMAP Output file to FASTA file |
1.0.0 |
16.01 |
|
|
Runs EvolMAP for longer (bigger) jobs. |
1.0.0 |
16.01 |
|
|
Modifies EvolMAP Output to exclude specific species. |
1.0.0 |
16.01 |
|
|
Convert Aligned FASTA to phylip Extended |
1.0.0 |
16.01 |
|
|
Run Phylomatic |
1.0.1 |
16.01 |
|
|
Convert Aligned FASTA to phylip Extended |
1.0.0 |
16.01 |
|
|
Pruning taxa from a tree or multiple trees |
1.0.0 |
16.01 |
|
|
Maximum Likelihood Analysis |
7.2.8 |
16.01 |
|
|
clearcut: Generate Neighbor Joining phylogeny. Input can be fasta or phytab format. |
1.0.0 |
16.01 |
|
|
LB_pruner: Identify genes on very long branches. |
1.0.0 |
16.01 |
|
|
Removes characters in a sequence |
1.0.0 |
16.01 |
|
|
Converts fasta file with sequences from same species and gene family to phytab format |
1.0.0 |
16.01 |
|
|
hmmsearch :: search profile(s) against a sequence database. Produces a phytab output. |
3.0 |
16.01 |
|
|
Selection of best-fit models of protein evolution. |
2.4 |
16.01 |
|
|
e.g. to get peptides from ESTs |
0.0.1 |
16.01 |
|
|
Runs phylobayes |
1.0.1 |
16.01 |
|
|
Phytab RaXML - RaXML for phytab format |
1 |
16.01 |
|
|
JModelTest description here. |
1.0 |
16.01 |
|
|
Assembly of transcriptomes. |
1.0.1 |
16.01 |
|
|
Convert between phylogenetic tree file formats |
1.0.0 |
16.01 |
|
|
Multiple Sequence Alignment |
6 |
16.01 |
|
|
Pairwise distance between taxa in a phylogenetic tree |
1.0.0 |
16.01 |
|
|
Produces concatenated sequence file from phytab file of aligned sequences |
1.0.0 |
16.01 |
|
|
Use RAxML to calculate a phylogeny with Parsimony |
7.2.8 |
16.01 |
|
|
RAxML read placement - Produces a labeled tree from RAxML. |
7.2.8 |
16.01 |
|
|
hmmbuild :: profile HMM construction from multiple sequence alignments in phytab format. |
3.0 |
16.01 |
|
|
Bayesian evolutionary analysis by sampling trees. |
1.7.2 |
16.01 |
|
|
Convert between phylogenetic tree file formats |
1.0.0 |
16.01 |
|
|
Multiple Sequence Alignment |
6 |
16.01 |
|
|
Pairwise distance between taxa in a phylogenetic tree |
1.0.0 |
16.01 |
|
|
Produces concatenated sequence file from phytab file of aligned sequences |
1.0.0 |
16.01 |
|
|
Use RAxML to calculate a phylogeny with Parsimony |
7.2.8 |
16.01 |
|
|
RAxML read placement - Produces a labeled tree from RAxML. |
7.2.8 |
16.01 |
|
|
hmmbuild :: profile HMM construction from multiple sequence alignments in phytab format. |
3.0 |
16.01 |
|
|
Bayesian evolutionary analysis by sampling trees. |
1.7.2 |
16.01 |