Repository gembassy
Name: gembassy
Owner: ktnyt
Synopsis: GEMBASSY wrapper tools
This is a wrapper for the EMBOSS associated software (EMBASSY) package "GEMBASSY", containing tools for accessing the G-language Web Services.
Content homepage: http://www.g-language.org/gembassy/
Development repository: https://github.com/ktnyt/gembassy
Link to this repository: https://toolshed.g2.bx.psu.edu/view/ktnyt/gembassy/8947fca5f715
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/ktnyt/gembassy
Type: unrestricted
Revision: 2:8947fca5f715
This revision can be installed: True
Times cloned / installed: 508

Contents of this repository

Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
Name Description Version Minimum Galaxy Version
Runs given perl script text 1.0.0 any
Runs given perl script file 1.0.0 any
Multiple sequence alignment using MUSCLE 1.0.2 any
Finds tRNA genes using tRNAscan-SE 1.0.2 any
Largest clique program using clique 1.0.2 any
Predicts transmembrance topology and signal peptides using Phobius 1.0.2 any
Nucleic acid sequence Distance Matrix program using dnadist 1.0.2 any
Compute genetic distances from gene frequencies using gendist 1.0.2 any
Fetch a set of entries in a defined format and style 1.0.2 any
Predicts protein localization for PSORT 1.0.2 any
Finds genes in prokaryotic genomes using GeneMarkhmm 1.0.2 any
Generation of sequence logos using WebLogo 1.0.2 any
Predicts secondary structure of single starnd RNA or DNA using RNAfold 1.0.2 any
Estimates nucleotide phylogeny by maximum likelihood using dnaml 1.0.2 any
Phylogenies from distance matrix by N-J or UPGMA method using neighbor 1.0.2 any
Estimates nucleotide phylogeny by maximum likelihood using dnamlk 1.0.2 any
Restriction site maximum Likelihood method utilizinig restml 1.0.2 any
Fetch an entry in a defined format and style 1.0.2 any
DNA parsimony algorithm using dnapars 1.0.2 any
Penny algorithm, branch-and-bound using penny 1.0.2 any
Nucleic acid sequence Invariants method using dnainvar 1.0.2 any
Fitch-Margoliash and Least-Squares Distance Methods using fitch 1.0.2 any
DNA compatibility algorithm using dnacomp 1.0.2 any
Search similar sequences in public repositories using SSEARCH 1.0.2 any
Multiple sequence alignment using MAFFT 1.0.2 any
Multiple sequence alignment using T-COFFEE 1.0.2 any
Mixed parsimony algorithm using mix 1.0.2 any
Search similar sequences in public repositories using BLAST 1.0.2 any
Protein distance algorithm using protdist 1.0.2 any
Mapping experimental data on PathwayProjector 1.0.2 any
Gene frequency and continuous character Maximum Likelihood using contml 1.0.2 any
Finds genes in prokaryotic genomes using Glimmer 1.0.2 any
Predicts protein localization for PSORT2 1.0.2 any
Penny algorithm Dollo or polymorphism using dolpenny 1.0.2 any
Fitch-Margoliash method with contemporary tips using kitsch 1.0.2 any
Protein parsimony algorithm using protpars 1.0.2 any
Predicts RNA 2D structure using CentroidFold 1.0.2 any
Predicts protein localization for PSORT B 1.0.2 any
Penny algorithm for DNA using dnapenny 1.0.2 any
Bootstrapped sequences algorithm using seqboot 1.0.2 any
Multiple sequence alignment using Kalign 1.0.2 any
Predicts protein localization for WoLF PSORT 1.0.2 any
Dollo and polymorphism parsimony algorithm using dollop 1.0.2 any
Calculates the frequency of optimal codons (Fop) 1.0.2 any
Calculates a measure of synonymous codon usage evenness (Ew) 1.0.2 any
Calculates and graphs the sequence conservation using Kullback-Leibler divergence (relative entropy) 1.0.2 any
Calculates strand bias of bacterial genome using B1 index 1.0.2 any
Identifies predicted highly expressed gene 1.0.2 any
Calculates consensus in given array of sequences 1.0.2 any
Calculates and graphs the sequence conservation using information content 1.0.2 any
Calculates and plots the GC skew of the input sequence 1.0.2 any
Calculates and plots the gene strand bias of the given genome 1.0.2 any
Calculates and plots the GC skew of the input sequence 1.0.2 any
Calculates codon adaptation index for each gene 1.0.2 any
Calculates the intrinsic codon deviation index (ICDI) 1.0.2 any
Converts a sequence to PNG image 1.0.2 any
Calculates strand bias of bacterial genome using B2 index 1.0.2 any
Predicts the replication origin and terminus in bacterial genomes 1.0.2 any
Creates a Chaos Game Representation of a given sequence 1.0.2 any
Creates randomized sequence with conserved k-mer composition 1.0.2 any
Calculates the effective number of codons (Nc) 1.0.2 any
Calculates and plots the GC content along the given genome 1.0.2 any
Extracts conserved oligomers per position using Z-score 1.0.2 any
Searches palindrome sequences 1.0.2 any
Prints out basic amino acid sequence statistics 1.0.2 any
Calculates strand bias of bacterial genome using delta GC skew index 1.0.2 any
Creates a position weight matrix of oligomers around start codon 1.0.2 any
Gets the replication arm name (left or right) from the given position 1.0.2 any
Calculates the scaled chi-square 1.0.2 any
Calculates the 'relative adaptiveness of each codon' (W) 1.0.2 any
Displays a graph of nucleotide contents around start and stop codons 1.0.2 any
Counts the number of given oligomers in a sequence 1.0.2 any
Draws DNA Walk map of the genome 1.0.2 any
Calculates dinucleotide usage 1.0.2 any
Calculates and graphs the sequence conservation using Shanon uncertainty (entropy) 1.0.2 any
Searches NCBI Entrez 1.0.2 any
Prints out basic nucleotide sequence statistics 1.0.2 any
Calculates oligonucleotide usage (genomic signature) 1.0.2 any
Calculates strand bias of bacterial genome using linear discriminant analysis (LDA) 1.0.2 any
Draws the map of the genome (version 3) 1.0.2 any
GC Skew Index: an index for strand-specific mutational bias 1.0.2 any
Retrieves various gene features from genome flatfile 1.0.2 any
Calculates the strength of selected codon usage bias (S) 1.0.2 any
Calculates the P2 index of each gene 1.0.2 any
Calculates various indece of amino acid usage 1.0.2 any
Searches oligomers in given sequence 1.0.2 any
Gets the positions of replication origin and terminus 1.0.2 any
Calculates and plots the GC skew in different regions of the given genome 1.0.2 any
Creates an image showing all k-mer abundance within a sequence 1.0.2 any
Calculates the distance between two loci in circular chromosomes 1.0.2 any
Checks the periodicity of certain oligonucleotides 1.0.2 any
Calculates the codon bias index (CBI) 1.0.2 any
Calculates the codon usage bias related to translation optimization (delta ENC) 1.0.2 any
Calculates base usage indices for protein-coding sequences 1.0.2 any
Calculates and plots the GC skew of the input sequence 1.0.2 any
Calculates various kinds of amino acid and codon usage data 1.0.2 any
Gets the strand name (leading or lagging) from the given position 1.0.2 any
Draws circular map of the genome 1.0.2 any
Retrieves various gene features from genome flatfile 1.0.2 any

Categories
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis