Software

• 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, released 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 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. It utilizes the structural components of RNA to help build 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.