thlee / SNPhylo

A pipeline to generate a phylogenetic tree from huge SNP data

http://chibba.pgml.uga.edu/snphylo/

thlee/SNPhylo Issues

http://chibba.pgml.uga.edu/snphylo/ 404 Not Found
Updated 10 months ago3
Invalid command line Unknown option phyi
Updated a year ago
Error in constructing bootstrapped tree
Updated a year ago8
http://chibba.pgml.uga.edu/snphylo/ does not exist!
Updated a year ago
Broken links in documentation
Updated 2 years ago1
Species name are too long; sequence is too short after default SNPs pruning
Updated 2 years ago
Error: The length of sequence is too long (> 50000 bp) to construct a tree!
Updated 2 years ago7
HapmapDiploid issue
Updated 2 years ago
IndexError: list index out of range
Closed 6 years ago3
IndexError: list index out of range
Updated 2 years ago1
VCF format problem
Updated 2 years ago
Error in .InitFile2
Updated 3 years ago3
Version reported by setup.sh is misleading
Updated 3 years ago
Error: Invalid length of dimension of 'val'.
Updated 3 years ago3
Error in scan.vcf.marker(fn, method)
Updated 3 years ago1
vcf.file is too small to run this script!
Updated 4 years ago1
python version
Updated 4 years ago1
SNPHYLO install problem for linux (CentOS 6)
Updated 4 years ago9
/usr/bin/R: No such file or directory
Updated 4 years ago
How to keep all the bootstrap trees
Updated 4 years ago
There are too small number of SNP data in the file
Updated 4 years ago9
Error: package or namespace load failed for 'gdsfmt'
Updated 5 years ago
Error: There are too small number of SNP data in the file
Updated 5 years ago3
error message: phylip/exe/dnaml.app: is a directory
Updated 5 years ago1
Exluding all SNPs on non-autosomes
Updated 5 years ago7
SNPhylo installed by phylip is a directory not an app
Updated 5 years ago1
How do you use this software?
Updated 5 years ago
Error in read.gdsn(index.gdsn(gdsobj, "genotype"))[, snp.idx] :
Updated 5 years ago2
SNPylo - phylogenetic tree construction problem
Updated 5 years ago1
ERROR in running SNPhylo
Updated 6 years ago2
Error in pml(newick, phylip) : tree must have unique labels!
Updated 6 years ago1
small number of SNPs
Updated 6 years ago2
Phylip compilation error on Mac OS
Updated 6 years ago7
Error getting the bootstrapped tree
Updated 6 years ago
error message when running snphylo.sh
Updated 7 years ago1
How long does the tool run for 1000 bootstraps of 30000 SNPs in PC?
Updated 7 years ago
the test data "soybean.hapmap" was faild
Updated 7 years ago1
did not have DP information and scaffolds not showing error
Updated 7 years ago8
how to use SNPhylo without knowing the reference genome
Updated 8 years ago
R function gds2fasta generates switched sequence?
Closed 8 years ago2
Error: unexpected '<' in "<"
Closed 8 years ago1
multi-alleli sites allowed?
Updated 8 years ago1
Warning: all SNP positions do not have DP information.
Updated 8 years ago5
Error: This program has caused a Segmentation fault.
Updated 8 years ago1
ValueError: invalid literal for int() with base 10: '.'
Closed 8 years ago6
Chromosome IDs
Closed 10 years ago2
snphylo.sh: line 232 possible typo
Updated 10 years ago2
convert_fasta_to_phylip.py does not work as expected for long species names
Updated 10 years ago1