Joseph F. Ryan (@josephryan)
github

josephryan

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  • Stars
    star
    144
  • Global Rank 158,553 (Top 6 %)
  • Followers 53
  • Following 7
  • Registered almost 12 years ago
  • Most used languages
    Perl
         86.2 %
    Roff     3.4 %
    Shell
         3.4 %
    R
         3.4 %
    HyPhy     3.4 %
  • Location 🇺🇸 United States
  • Country Total Rank 36,278
  • Country Ranking
    HyPhy     5
    Perl
         155
    Roff     579
    R
         7,851

Top repositories

1

estimate_genome_size.pl

Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish
Perl
56
star
2

alien_index

identify potential non-animal transcripts in animal transcriptomes
Perl
11
star
3

sowhat

Program to run the SOWH test (likelihood-based test used to compare tree topologies which are not specified a priori)
Perl
11
star
4

FastqSifter

Separate contaminating reads from FASTQ files (e.g., mitochondria, symbionts, bacterial or human contaminants)
Perl
9
star
5

phylotocol

template, example, and instructions on how to make an a priori phylogenetic protocol
8
star
6

Hernandez_Ryan_2021_Recoding

Simulation study of recoding effectiveness
Perl
7
star
7

leapfrog

identify BLAST hits between two datasets by employing a third intermediate dataset
Perl
6
star
8

isoblat

use RNA transcripts to assess assembly - this program parses the output of a BLAT run of transcriptome vs. a genome. It returns 1) Total % mapped, 2) average %coverage of a mapping, and 3) number of transcripts mapping to a single contig/scaffold. It is simple to run. Just run the blat (transcripts vs. genome) and then run the script with the blat-output and your transcript-fasta-file as arguments.
Perl
5
star
9

2017-DEEPC_Ctenophora

HyPhy
4
star
10

matemaker

make artificial mate pairs from long sequences for scaffolding
Perl
3
star
11

exoblast

compare genome assemblies using sequence similarity to transcript or protein sequences from a different species.
Perl
2
star
12

RyanLabUnixBestPractices

A set of conventions we use in our lab
2
star
13

SeaCucumberPhylogenomics

Sea cucumber phylogenomics
Perl
2
star
14

hmm2aln.pl

script to automate gene family phylogeny based using HMM
Perl
2
star
15

2018-Pastrana_etal_SpongeParaHoxAnalyses

files related to testing for existance of sponge ParaHox genes
Perl
1
star
16

Beroe_genome

Perl
1
star
17

ctenophore_innexins

Analyses of the innexins of ctenophores
Roff
1
star
18

check_for_gold_in_short_seqs

Often before finalizing genome assemblies, short seqs are removed. This script uses transcripts to find bits missing in the long but present in the short. Note:GenBank requires removal of seqs shorter than 200.
Perl
1
star
19

2019-DeBiasse_etal_CorellaGenome

Corella genome project scripts, phylotocol, etc.
Perl
1
star
20

tmppolar

temporary staging area for polar workshop update
Perl
1
star
21

2017b_Sasson_and_Ryan

A reconstruction of sexual modes throughout animal evolution
R
1
star
22

2018-Hernandez_and_Ryan_HGT

files associated w 2017 HGT study by Hernandez and Ryan
Perl
1
star
23

Steinworth_CnidarianHox

Cnidarian Hox Phylotocol and scripts
Perl
1
star
24

pal2nal_gblocker

produce a nucleotide alignment that corresponds with a GBLOCKED amino-acid alignment
Perl
1
star
25

Ohdera_et_al_2018

3 Acraspeda genomes
Perl
1
star
26

RyanLabShortReadAssembly

Our pipeline for assembling short reads
Perl
1
star
27

DeBiasse_cnidophylogenomics

Perl
1
star
28

phyloconverge

an algorithm to look for convergent signals in phylogenetic trees
Perl
1
star
29

make_subalignment

This script takes a prefix of a subset of (our ingroup) taxa and will return an alignment of only those genes within the clade descended from the most recent common ancestor of all genes with the specified prefix.
Perl
1
star
30

2017-Kayal_et_al

Shell
1
star
31

SELECTINGS

A pipeline to detect positive Darwinian selection in large datasets
Perl
1
star