thlee SNPhylo issues - Githubissues

thlee / SNPhylo

A pipeline to generate a phylogenetic tree from huge SNP data

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

GNU General Public License v2.0

82 stars 37 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Dated tree

#54 timurrxxcd opened 5 days ago
0
Invalid command line Unknown option phyi

#52 tcd11221 opened 1 year ago
7
Adding changes from 2to3

#51 snehring opened 1 year ago
0
http://chibba.pgml.uga.edu/snphylo/ does not exist!

#50 liuyadong2023 opened 1 year ago
0
Species name are too long; sequence is too short after default SNPs pruning

#49 hungweichen0327 opened 1 year ago
0
HapmapDiploid issue

#48 kim750a11 opened 2 years ago
0
VCF format problem

#47 aslangabriel opened 2 years ago
0
http://chibba.pgml.uga.edu/snphylo/ 404 Not Found

#46 Varisha-RIVM opened 2 years ago
3
Version reported by setup.sh is misleading

#45 Ghepardo opened 3 years ago
0
Broken links in documentation

#44 Ghepardo opened 3 years ago
1
When using an outgroup, the program fails silently. This fixes the problem!

#43 jasongallant opened 4 years ago
0
/usr/bin/R: No such file or directory

#42 qbdong opened 4 years ago
0
python version

#41 qbdong opened 4 years ago
1
How to keep all the bootstrap trees

#40 SC-Duan opened 4 years ago
0
vcf.file is too small to run this script!

#39 Yichel518 opened 4 years ago
2
Error: package or namespace load failed for 'gdsfmt'

#38 emrosenthal17 opened 4 years ago
0
Error: Invalid length of dimension of 'val'.

#37 YXXEMXL opened 4 years ago
3
Error in constructing bootstrapped tree

#36 tuchino opened 4 years ago
8
error message: phylip/exe/dnaml.app: is a directory

#35 zuzmus opened 4 years ago
1
Error: There are too small number of SNP data in the file

#34 fedebian91 opened 4 years ago
3
How do you use this software?

#33 gholl0 opened 4 years ago
0
Error in scan.vcf.marker(fn, method)

#32 ketienne opened 5 years ago
1
SNPhylo installed by phylip is a directory not an app

#31 kcairns opened 5 years ago
1
Exluding all SNPs on non-autosomes

#30 daneshnedaie opened 5 years ago
7
Error in pml(newick, phylip) : tree must have unique labels!

#29 fjptwenger opened 5 years ago
1
Error in .InitFile2

#28 rosbashlab opened 5 years ago
3
ERROR in running SNPhylo

#27 y842739756 opened 5 years ago
2
Error getting the bootstrapped tree

#26 RS924 opened 6 years ago
0
How long does the tool run for 1000 bootstraps of 30000 SNPs in PC?

#25 wjaratlerdsiri opened 6 years ago
0
IndexError: list index out of range

#24 stly1996 closed 5 years ago
3
Error: The length of sequence is too long (> 50000 bp) to construct a tree!

#23 Yoko-Hira opened 6 years ago
9
Correct info in help for 20160204 release

#22 kiwiroy opened 6 years ago
0
error message when running snphylo.sh

#21 christinawu2008 opened 6 years ago
1
the test data "soybean.hapmap" was faild

#20 moko-moko opened 7 years ago
1
SNPHYLO install problem for linux (CentOS 6)

#19 moko-moko opened 7 years ago
9
Add options to adjust the windows for LD pruning.

#18 jashapiro opened 7 years ago
0
SNPylo - phylogenetic tree construction problem

#17 Wijayananda opened 7 years ago
1
how to use SNPhylo without knowing the reference genome

#16 victorkaka opened 7 years ago
0
Phylip compilation error on Mac OS

#15 bauchetg opened 7 years ago
7
R function gds2fasta generates switched sequence?

#14 dandaman closed 7 years ago
2
There are too small number of SNP data in the file

#13 hechuweiran opened 8 years ago
9
Error: unexpected '<' in "<"

#12 ghost closed 8 years ago
1
multi-alleli sites allowed?

#11 MichelMoser opened 8 years ago
1
Error in read.gdsn(index.gdsn(gdsobj, "genotype"))[, snp.idx] :

#10 grendon opened 8 years ago
2
small number of SNPs

#9 jianlizhao opened 8 years ago
2
Error: This program has caused a Segmentation fault.

#8 teyden opened 8 years ago
1
ValueError: invalid literal for int() with base 10: '.'

#7 lauscherin closed 8 years ago
6
IndexError: list index out of range

#6 jlcaldu opened 9 years ago
1
did not have DP information and scaffolds not showing error

#5 sandeshsth opened 9 years ago
8
Warning: all SNP positions do not have DP information.

#4 wcudude14 opened 9 years ago
5