Apps by bhaas

PASA

FREE
The Program to Assemble Spliced Alignments (PASA) is used to automatically incorporate ESTs and full-length cDNAs into gene structure annotations, in the process annotating UTRs, alternative splicing variations, and polyadenylation sites.

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Trinity RNA-Seq Assembly

FREE
The Trinity RNA-Seq Assembly project provides software solutions targeted to the reconstruction of full-length transcripts and alternatively spliced isoforms from Illumina RNA-Seq data.

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EVidenceModeler (EVM)

FREE
EVidenceModeler (aka EVM) combines ab initio gene predictions and spliced protein and transcript alignments into weighted consensus gene structure predictions.

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MicrobiomeUtilities

FREE
A set of software utilities for processing and analyzing 16S rRNA genes including generating NAST alignments, chimera checking, and assembling paired 16S rRNA reads according to reference sequence homology.

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TransposonPSI

FREE
TransposonPSI is an analysis tool to identify protein or nucleic acid sequence homology to proteins encoded by diverse families of transposable elements.

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DAGchainer 06

FREE
DAGchainer identifies chains of gene pairs sharing conserved order between genomic regions, by identifying paths through a directed acyclic graph (DAG).

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slclust

FREE
slclust: a utility that performs single-linkage clustering with the option of applying a Jaccard similarity coefficient to break weakly bound clusters into distinct clusters.The slclust utility is written in ANSI C++.

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AAT Genome Spliced Alignment

FREE
The AAT (Analysis and Annotation Tool) spliced genome alignment package now available as Open Source.

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SyntenyMiner 0001

FREE
SyntenyMiner provides a user interface to navigate matches between multiple genome sequences.

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