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- Scallop Parameter Advising: A method for automatically choosing the parameters for transcriptome assembly (link)
Developed in Perl. This is a wrapper around Scallop which relies on several other tools. Scallop itself is written in C++ but is available in binary format for easy installation. The configuration files provided were learned using simulated annealing and do not need to be retained to use advising.
- Facet : Multiple alignment accuracy estimation using a combination of simple features (link)
Developed in Perl and Java. This program learns a linear alignment accuracy estimation function based on easily computable feature values. Each of the values is computed independently. The coefficients of the estimation function are learned using a quadratic program solver based on structurally aligned references.
- Opal v3.0 : Software for aligning multiple sequences (link)
Developed in Java. The Opal alignment tool was originally published in 2007. Version 3.0 of the program, re-leased Summer 2015, includes new functionality to allow the alignment step to be easily integrated with Facet and be seamlessly used for the task of parameter advising.
- SICLE : quickly identifying sister clades in a phylogeny (link)
Developed in C++ this program is used for high throughput phylogeny analysis. Given an input tree in newick format, and a search term, SiClE identifies if the tree is monophyletic for a the search prefix and returns the monophyletic sisters if they exist. Source code, examples and a detailed description are available online.
- PMFastR : Aligning RNA using secondary structure compatibility (link)
Developed in C++ this program is based on FastR by S.H. Zhang et al. Utilizing the structural components of RNA to help builds a multiple alignment of these sequences. It also reduces the memory consumption of the original program from quadratic space to near linear. We also reengineered it to run in a multi-processor environment.