Bioinformatics tools developed in the context of PEP

Tools for organelle genomics

Stand-Alone Tools:

1. TreeBlaster

1. Program Description: An all in one web-based multiple alignment and phylogenetic tree builder. The input is a single sequence and allows the user to eventually construct a basic phylogenetic tree. The tool works by blasting NCBI databases and then adding buttons to each BLAST hit returned. These buttons allow the user to run iterative BLASTs using the BLAST hit as input, and to save the BLAST hits as sequences to a growing multiple alignment file. When a multiple alignment file is complete, the user proceeds to the tree-building phase that pipelines the sequences through ClustalW, puzzle, weighbor, and consense to build a basic phylogenetic tree.
2. System Requirements: CGI script capability, perl, unix OS (including a "/tmp" directory), web browser, and locally installed phylogenetic software (puzzle5, clustalw, consense, weighbor, ) 
3. Download



2. PhyloWiz

1. Program Description: A command line program that starts with files in nexus format and creates phylip files containing user-defined subsets of characters and taxa, and then does some automated phylogenetic analyses. The user inputs names of nexus files and names of taxa lists to include or exclude from the analysis. Character sets or exclusion-sets are read from the nexus files and directories are created grouping nexus files together by use of common character sets and taxa lists. Phylogenetic analyses are then performed on some or all of these newly created files. The options for phylogenetic analyses are distance analysis (puzzle->fitch->weighbor->consense), distance bootstrapping (puzzle->fitch->seqboot-> puzzleboot), and ML analysis (puzzle->pmbml->phyml). 
   
2. System Requirements:  perl, interactive shell, unix OS or Mac OS X, and locally installed phylogenetic software: puzzle5, consense, clustalw, weighbor, fitch, paup4.0, puzzleboot, seqboot, pmbml, and phyml. NOTE: It is possible to use other parts of the program without all software installed!
3. Download



3. CrossBlaster

1. Program Description: A web-based program for running iterative BLASTs on any two local data sets of sequences. The user inputs up to five directory names, each of which contains FASTA sequence files which will serve as BLAST inputs. Either these directories must contain only sequence files, or all sequence files must have a common prefix that is provided to the program. For a database to BLAST against, the user either inputs a concatenated FASTA file or else the names of directories containing FASTA sequence files that are used in creating the database to BLAST against. The output of the program is a webpage containing a table summarizing the BLAST data. The table contains three columns: input sequence name, name of top hit (with a link to the BLAST output), and E-value.
   
2. System Requirements: CGI script capability, perl, unix OS (including a "/tmp" directory), blastall and formatdb software installed locally, and a web browser 
3. Download
   



4. Sliding Window Programs:

1. Amino Acid Frequency

1. Program Description: A command-line program that performs a sliding window analysis on amino acid frequency. The program works by taking in a file with any number of concatenated FASTA sequences and calculating the amino acid frequency over all possible windows for each FASTA file. The user inputs the filename, window size to use, and amino acid to search for
2. System Requirements: perl, interactive shell, and unix OS or Mac OS X
3. Download



2. Kyte-Doolittle Hydrophobicity Averages

1. Program Description; A command-line program that performs a sliding window analysis by calculating average Kyte-Doolittle hydrophobicity value for each window. The program works by taking in a file with any number of concatenated FASTA sequences and calculating the average Kyte-Doolittle over all possible windows for each FASTA file. The user inputs a filename as well the the sliding window size to use.
2. System Requirements: perl, interactive shell, and unix or Mac OS X
3. Download 



3. Consensus Sequence Finder

1. Program Description: A command-line program that performs a sliding window analysis by searching for any matches to a consensus sequence that are above some cut-off percent. The program works by taking in a file of FASTA sequences and a file with the consensus sequence, and the cut-off percent to be considered a match. The consensus sequence may contain any of the amino acid symbols as well as {o, l, '.' , '+', a, c, h, '-', s, p, u, t} -> the meaning of each symbol is included in the README file.
2. System Requirements: perl, interactive shell, and unix or Mac OS X
3. Download
   



5. AutoFact

1. AutoFACT is a program that analyses nucleotide and protein sequence data, deriving informative functional descriptions by combinining multiple BLAST reports from a selection of databases. AutoFACT assigns functional information, enzyme clasees, and Gene Ontology terms where possible. For more information, consult the AutoFACT homepage.
2. Download

AnaBench:

• All software is distributed "as is" and comes with no guarantees 
• Users are free to modify the software provided credit is given

Back to Evolutionary Genomics at the Université de Montréal