issues
search
LANL-Bioinformatics
/
PhaME
Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (genes under positive selection) using CDS SNPs.
GNU General Public License v3.0
31
stars
15
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
I suggest updating the "phame" file
#28
SerhEL
opened
3 months ago
0
Empty matrix files
#27
sophiakenney
opened
10 months ago
6
{genome}_cds.gff wrong coordinates
#26
JuanTrinidad
opened
10 months ago
3
uncaught exception from user code:
#25
zahidul-islam-nahid
closed
11 months ago
1
Pal2nal ERROR: inconsistency
#24
LeoVincenzi
closed
10 months ago
5
Pal2nal translation of large multi-fasta files produces a codon translated file where some of the sequences are half length of the average
#23
VectorFrankenstein
closed
9 months ago
1
ERROR: number of input seqs differ (aa: 41; nuc: 0)!!
#22
Rhia15
opened
1 year ago
1
t1_all_snp_alignment.fna: No such file or directory
#21
mainguyenhuyen
closed
9 months ago
1
SNPsfilter???
#20
hbadrane
opened
1 year ago
0
SAMtools 1.15 is a more recent release than 1.3.
#19
davidjstudholme
opened
2 years ago
5
project_all_alignment.fna file not found
#18
molbio7
opened
2 years ago
1
error running get_repeat_coords.pl
#17
pdimens
opened
2 years ago
0
Issue with Phame tree topology
#16
ChloeAmbroset
opened
2 years ago
0
Uncaught exception from user code: Error running buildSNPDB.pl
#15
dineshkumarsrk
opened
3 years ago
1
buildSNPdb
#14
aemjunior
opened
3 years ago
1
Can't locate Bio/SeqIO.pm in @INC
#13
gpmoran
opened
3 years ago
2
Ability to work with compressed fastqs!
#12
caonetto
opened
3 years ago
0
samtools issue
#11
civanovich-senck
opened
3 years ago
10
Update PhaME.pm
#10
rohith-molsys
opened
4 years ago
0
minor bug fixes
#9
mshakya
closed
4 years ago
0
minor merge
#8
mshakya
closed
4 years ago
0
BWA is the main aligner now
#7
mshakya
closed
4 years ago
0
CDS update
#6
mshakya
closed
4 years ago
0
merging
#5
mshakya
closed
5 years ago
0
Merge pull request #5 from LANL-Bioinformatics/master
#4
mshakya
closed
5 years ago
0
readme instruction changes
#3
mshakya
closed
5 years ago
0
Pull request #1
#2
mshakya
closed
5 years ago
0
all my changes
#1
mshakya
closed
6 years ago
0