Wheeler Lab (TravisWheelerLab)

Wheeler Lab

TravisWheelerLab

Geek Repo

Home Page:http://wheelerlab.org

Twitter:@TravisJWheeler

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Wheeler Lab's repositories

AvxWindowFmIndex

A fast, AVX2 and ARM Neon accelerated FM index library

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nail

Nail is an Alignment Inference tooL

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drug-sniffer

Sniffing out new drugs

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ULTRA

ULTRA Locates Tandemly Repetitive Areas

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BATH

Better Alignments with Translated HMMER

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polyA

Automatically Adjudicate Any And All Arbitrary Annotations, Astutely Adjoin Abutting Alignments, And Also Amputate Anything Amiss (AAAAAAAAAAAAAAAA)

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Mirage

Mirage generates multiple sequence alignments of proteoforms by mapping sequences back to their coding regions on the genome and then compressing those mappings into alignments.

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NINJA

Nearly Infinite Neighbor Joining Application

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VIBES

Viral Integrations in Bacterial genomES

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disco

Classifies sound bursts with machine learning.

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DIPLOMAT

Deep learning-based Identity Preserving Labeled-Object Multi-Animal Tracking (Beta)

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FastaVector

A C library for reading/writing entire fasta files. Fasta files are loaded into internal buffers that store all headers and sequences such that each sequence and header can be found via a simple lookup function.

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HAVAC

Hardware Accellerated Viterbi Additional Coprocessor (HAVAC) is an FPGA-accellerated implementation of the Single-segment Ungapped Viterbi algorithm for use in nucleotide sequence homology search

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mmoreseqs

Fast/sensitive protein sequence similarity search. Slightly slower than mmseqs2, much more sensitive.

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mmoreseqs-legacy

Pruned Forward-Backward implementation of profile HMM alignment

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P7HmmReader

A simple C file reader for P7 profile HMM files generated by HMMER3 and other tools

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trans-hmmer

Fork of HMMER, containing translated search variants: hmmsearcht and hmmscant

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WASITAMATchISAW

Approximate palindromes lead to overstated false match rates in benchmarks using reversed sequences

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Diviner

Using Mirage2 MSAs to uncover exons hiding in plain sight

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easel

Sequence analysis library used by Eddy/Rivas lab code

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easel-FraHMMER

Sequence analysis library used by Eddy/Rivas lab code

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easel-FraHMMER-dead-end

Sequence analysis library used by Eddy/Rivas lab code

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geomxrename

Rename files for use by GeoMX NGS Pipeline app on BaseSpace (Illumina)

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nail-benchmarks

A collection of reproducible benchmarks for nail

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slack-msgs

Backup Slack messages

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