Johan Nylander (@nylander)
github

nylander

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  • Stars
    star
    131
  • Global Rank 170,475 (Top 6 %)
  • Followers 74
  • Following 36
  • Registered over 12 years ago
  • Most used languages
    Perl
         52.0 %
    Shell
         28.0 %
    C
         8.0 %
    Python
         4.0 %
    R
         4.0 %
    OpenEdge ABL     4.0 %
  • Location πŸ‡ΈπŸ‡ͺ Sweden
  • Country Total Rank 1,803
  • Country Ranking
    OpenEdge ABL     4
    Perl
         9
    R
         307
    Shell
         354
    C
         372
    Python
         4,266

Top repositories

1

catfasta2phyml

Concatenates FASTA formatted files to one "phyml" (PHYLIP) formatted file
Perl
64
star
2

MrModeltest2

C program for selecting DNA substitution models using PAUP*
C
17
star
3

Burntrees

Perl scripts for manipulating output from phylogenetic MCMC software (MrBayes, BEAST, PhyloBayes, etc)
Perl
11
star
4

translate_fasta_headers

Translate long fasta headers to short - and back!
Perl
4
star
5

beast2phy

Convert output trees from BEAST to other formats
Perl
4
star
6

grepfasta

Yet another grep for FASTA formatted files - with regexp capacity!
Perl
3
star
7

get_fasta_info

Some useful summary tools for FASTA formatted files
Shell
3
star
8

plotMCMCoutput

Shell scripts (bash) for plotting MCMC output (e.g., from MrBayes v.3, BEAST, etc) using gnuplot
OpenEdge ABL
2
star
9

reorient_fasta

Reverse-complement DNA sequences as needed in relation to a reference. Based on blastn.
Perl
2
star
10

fastagap

Remove or replace gaps in fasta formatted files
Perl
2
star
11

Check_MD5SUMS

Check md5 sums for all .md5 and MD5SUMS files found in directory tree
Shell
2
star
12

ptemplate

ptemplate -- A project template
Shell
1
star
13

saturation.plot

Code for for displaying the relationship between the uncorrected (P-) distance and the distance on a phylogenetic tree
R
1
star
14

MrAIC

Perl script for selecting DNA substitution models using PhyML
Perl
1
star
15

consensus-sequence

Perl
1
star
16

FastEAR

FastEAR - Fast(er) Extraction of Alignment Regions from FASTA
Shell
1
star
17

fastp-cleaning

Clean fastq files with fastp
Python
1
star
18

taxid2scientific_name

Get scientific name from Genbank taxon ID - or the other way around
Perl
1
star
19

phy2fas

Phylip to fasta converter using BioPerl
Perl
1
star
20

Align-and-trees-parallel-workflow

Script for running a "standard" phylogenetic workflow on fasta-formatted input. In particular, parallel execution is done whenever possible.
Shell
1
star
21

efasta2fasta

Convert extended fasta (efasta) to fasta
Perl
1
star
22

Easy_webshare_on_UPPMAX

Easy file sharing on UPPMAX
Shell
1
star
23

DIVA-Dispersal-Vicariance-Analysis

Downloaded from SourceForge
C
1
star
24

pMrAIC

Parallel MrAIC
Perl
1
star
25

run-mrbayes-on-uppmax

Notes on running MrBayes on UPPMAX compute resources
Shell
1
star