Pinned Repositories
muscle
Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.
newick
Manipulate and generate figures for trees in Newick format
palmdb
Database of virus RdRP barcode sequences
palmscan
reseek
Protein structure alignment and search algorithm
spades_circular_contigs
Python script to identify circular contigs from SPAdes assembler.
syncmer
Validation of sycnmers compared to minimizers
urmap
URMAP ultra-fast read mapper
usearch12
Open-source usearch
usearch_old_binaries
Executable files for usearch versions 5 through 11, donated to the public domain
rcedgar's Repositories
rcedgar/muscle
Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.
rcedgar/usearch12
Open-source usearch
rcedgar/palmscan
rcedgar/reseek
Protein structure alignment and search algorithm
rcedgar/newick
Manipulate and generate figures for trees in Newick format
rcedgar/palmdb
Database of virus RdRP barcode sequences
rcedgar/syncmer
Validation of sycnmers compared to minimizers
rcedgar/spades_circular_contigs
Python script to identify circular contigs from SPAdes assembler.
rcedgar/usearch_old_binaries
Executable files for usearch versions 5 through 11, donated to the public domain
rcedgar/palm_annot
Scripts, HMMs and search databases for identifying and classifying viral RdRp sequences
rcedgar/rdrp_tree_experiments
Code, data and results for Muscle5 ensemble experiments on RdRp genus and phylum trees
rcedgar/renomad
Implementation of NOMAD (https://doi.org/10.1101/2022.06.24.497555)
rcedgar/circuclust
Clustering and alignment for circular sequences
rcedgar/palmscan2
rcedgar/jupiter
Generate "Jupiter" plots for circular genomes
rcedgar/re_coding_style
Robert C. Edgar's C++ coding style
rcedgar/balifam
Protein multiple sequence alignment benchmark
rcedgar/pylddt
Python script to calculate LDDT and DALI Z score from MSA plus structures
rcedgar/qscore
Compares a multiple alignment with a reference and reports accuracy scores.
rcedgar/retree
Python Newick tree format parser and Robinson-Foulds calculator (self-teaching exercise)
rcedgar/tara_oceans
Data and scripts to reproduce my analysis of Tara Oceans data
rcedgar/usearch12_documentation
Documentation for USEARCH v12
rcedgar/cmpairs
Parse infernal cmscan tbl file to find pairs of hits to same model on different strands
rcedgar/diamond
Accelerated BLAST compatible local sequence aligner.
rcedgar/HelloWorld
A C++ Hello World project, using CMake, and GitHub Actions
rcedgar/muscle_benchmark
rcedgar/regammon
RE-implementation of TD-Gammon
rcedgar/reseek_scop40
rcedgar/ribozy
Code for identifying candidate ribozyviria sequences
rcedgar/vcxproj2makefile
Simple python2 script to convert Microsoft Visual Studio C++ project to gcc Makefile