* '''Preconditions''': user has a query sequence representing a protein-coding gene.
** Method 1. User dowload pre-computed sequence family from databases. Example: [http://pfam.sanger.ac.uk/family?acc=PF0004
34 KB (4,831 words) - 16:08, 8 November 2011
...cterize gene families when starting with genomic sequence or clustered EST sequence ([[Family_Alignment_Documentation|Family Alignment Documentation]]). The cr
===Reconciling the Multiple Trees Created by Analyzing Genomes===
6 KB (876 words) - 16:23, 3 March 2008
a set of character data (e.g., a sequence alignment) along with a tree, and
...ht imagine that this useful information comes from plugging the nucleotide sequence information into an ''a priori'' biophysical model of the cell to predict i
41 KB (6,423 words) - 02:20, 30 March 2008
...l tools from the dart bioinformatics package to annotate multiple sequence alignments, train phylogenetic grammars, and vizualize this information in an Ajax-ena
...ki/index.php/Gbrowse Genome Browser] by dividing the single large image to multiple tracks. Phylogenetic information will also be represented as a new data tr
33 KB (4,999 words) - 21:12, 22 October 2010
...(GSoC) program, it is proposed that genetic haplotypes, multiple sequence alignments and phylogenetic trees be added as new information tracks to the browser. I
...ns, gaps and deletions. Web Miller’s Multiz program as well as the MAF (multiple alignment format) will be investigated. (Weeks 6-9)
8 KB (1,310 words) - 16:31, 21 December 2007
We already have a good sequence and alignment model.
# Sequence family analysis pipeline ([[Public:UseCases#Family_alignment:_identify_homo
16 KB (2,329 words) - 11:27, 5 September 2007
Compares phylogenetic or population genetic data alignments
** Combine analyses over multiple trees and/or characters
10 KB (1,339 words) - 13:17, 16 July 2008
...and associated data, but methods for tree manipulation, representation of multiple trees and metadata, and interfaces with other data formats (i.e. [[Suppor
...focusing on methods such as tree pruning, subsetting, and manipulation of multiple tree objects that are currently incomplete and will have the greatest impac
56 KB (8,424 words) - 21:11, 22 October 2010
...storing information about the trees themselves (such as branch lengths and multiple support values) along with data such as taxonomic and genomic annotations.
...cientists work in C++. The plan is therefore to translate the library into multiple other languages, including Java and R. (Perl, Python, and Ruby have been do
78 KB (11,838 words) - 16:25, 23 December 2010
:Nexml files can contain three different types of data (trees, alignments, and plain sequences), however BioPerl does not contain a single object tha
...forcing the user to parse the file three times - once each for sequences, alignments, and trees. These methods will make use of the methods above (e.g. Bio::Se
16 KB (2,526 words) - 14:55, 12 August 2009
...oc2010/nescent/t127230761053 Extending Jalview Capabilities to Support RNA Sequence Alignment Annotation and Secondary Structure Visualization]</span> ===
...structure viewer, and add the ability to import existing RNA sequences and alignments from the Rfam database.
65 KB (9,936 words) - 16:24, 23 December 2010
...dary structure viewer and the ability to import existing RNA sequences and alignments from the Rfam database will also be added.
* Coloring relevant to nucleotide alignments (pyrimidine, purine)
12 KB (1,917 words) - 04:51, 17 August 2010
...s to attempt this with small morphological matrices before moving to large sequence-based matrices.
:* TreeBASE is a large codebase, using a multiple-layer technology stack, and making changes to it requires getting familiar
80 KB (12,076 words) - 07:01, 17 December 2012
...//hyphy.org/ HyPhy] provides a popular package for molecular evolution and sequence statistical analysis. This project brings HyPhy workflows into the Galaxy s
'''Project:''' Extending Jalview Capabilities to Support RNA Sequence Alignment Annotation and Secondary Structure Visualization
5 KB (753 words) - 18:06, 22 October 2010
'''Abstract:''' With the prevalence of 16S sequence data there is a need for ecologists to classify different populations assoc
...VJ6X3RIV2Xoo9BJYX4rYIavIJt_ma1tTy8KY/edit Extend Jalview's support for RNA alignments, with a special emphasis on its communication with VARNA] ===
73 KB (11,176 words) - 10:19, 19 September 2012
===Extend PartitionFinder to automatically partition DNA and protein alignments===
...new algorithm to automatically split either user defined subsets or entire alignments into one or more new subsets using site-specific likelihoods under differen
65 KB (9,901 words) - 11:41, 14 February 2014
...ddress this, by providing methods to automatically partition morphological alignments.
In last year's GSoC, we implemented a method that automatically partitions alignments based on the features of the alignment itself, without the need for users t
57 KB (8,607 words) - 12:29, 28 February 2014