Robert Edgar

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.

usearch12. Open-source usearch

reseek. Protein structure alignment and search algorithm

urmap. URMAP ultra-fast read mapper

palmscan. C++

usearch_old_binaries. Executable files for usearch versions 5 through 11, donated to the public domain

newick. Manipulate and generate figures for trees in Newick format

palmdb. Database of virus RdRP barcode sequences

palm_annot. Scripts, HMMs and search databases for identifying and classifying viral RdRp sequences

viratax. Taxonomy classification of viral sequences / contigs

syncmer. Validation of sycnmers compared to minimizers

spades_circular_contigs. Python script to identify circular contigs from SPAdes assembler.

palmscan2. C++

rdrp_tree_experiments. Code, data and results for Muscle5 ensemble experiments on RdRp genus and phylum trees

taxxi. Taxonomy cross-validating by identity

re_coding_style. Robert C. Edgar's C++ coding style

renomad. Implementation of NOMAD (https://doi.org/10.1101/2022.06.24.497555)

pylddt. Python script to calculate LDDT and DALI Z score from MSA plus structures

circuclust. Clustering and alignment for circular sequences

jupiter. Generate "Jupiter" plots for circular genomes

scop40c. Python

usearch12_documentation. Documentation for USEARCH v12

null_model2. Python

tara_oceans. Data and scripts to reproduce my analysis of Tara Oceans data

qscore. Compares a multiple alignment with a reference and reports accuracy scores.

retree. Python Newick tree format parser and Robinson-Foulds calculator (self-teaching exercise)

balifam. Protein multiple sequence alignment benchmark

simple_paired_read_simulator. A simple paired-read simulator in stand-alone Python2