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DessimozLab
/
read2tree
a tool for inferring species tree from sequencing reads
MIT License
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18
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OMA not generating the marker genes
#64
evo-eco-gen
opened
5 days ago
3
Question: What is the question mark in the amoni acid sequence?
#63
YuWang07
opened
2 weeks ago
0
IndexError: tuple index out of range
#62
ppat818
opened
1 month ago
1
Adding samples to the yeast tree presented in Dylus et al. 2023.
#61
caonetto
closed
2 months ago
0
TypeError: cannot unpack non-iterable NoneType object
#60
pengyan19
opened
2 months ago
2
AttributeError when running OGset.py
#59
scuadros28
opened
4 months ago
11
BUG?: KeyError(s) when running read2tree
#58
almosnow
opened
4 months ago
3
for test dataset, tree topology matches but not branch lengths; is this ok?
#57
douglasgscofield
closed
5 months ago
2
Trouble in downloading OMA database
#56
xuliuouc
closed
5 months ago
5
Provide the dna and aa partitions in the output alignment
#55
ArielRodrig
closed
5 months ago
1
Applied read2tree to customer marker gene sets
#54
YuWang07
closed
6 months ago
6
QUESTION: Hetero sites.
#53
mudymudy
opened
7 months ago
0
How to create a tree with bootstrap?
#52
sly724
closed
7 months ago
2
Adding species but not repeating the mapping of existing species
#51
Yuqia
opened
7 months ago
1
Only R1 reads mapped for paired-end read input?
#50
Yuqia
closed
7 months ago
2
multiple threads for mapping multiple species
#49
Yuqia
closed
7 months ago
4
installation error
#48
laseulefourmie
closed
7 months ago
2
Error message with Conda installation instructions
#47
bernard-kim
closed
8 months ago
1
IndexError: list assignment index out of range in Mapper.py
#46
bernard-kim
opened
8 months ago
1
RuntimeError: generator raised StopIteration
#45
bernard-kim
opened
8 months ago
0
dna_reference not parsed when file extension is not .fa
#44
Banthandor
closed
8 months ago
1
Python version
#43
Banthandor
closed
8 months ago
1
Error for some reads when conducting mapping step
#42
GYQ-form
opened
10 months ago
4
cannot get dna from REST
#41
GYQ-form
closed
10 months ago
3
possible error in the help message of --sample_reads
#40
lilindu
opened
10 months ago
1
Installation issue using conda
#39
InfiniteLaugh
closed
10 months ago
2
can I change the tmp/ path ？
#38
LittleFrogHill
closed
10 months ago
1
[Question] Are very short insert sizes an issue?
#37
mptrsen
closed
7 months ago
5
OGs did not have any DNA
#36
Alfred-RRu
opened
10 months ago
4
KeyError in Alignment
#35
kodingkoning
closed
7 months ago
10
How to conduct 'Multiple species mode' of read2tree.
#34
Galaxy-228
closed
11 months ago
0
read2tree can't find corresponding CDS for each OMA group
#33
sci-study
opened
12 months ago
2
UnsatisfiableError when installing from conda
#32
kodingkoning
closed
11 months ago
3
error when map rna-seq to OMA db
#31
catslu
closed
1 year ago
1
bacteria_markergenes also mammalia
#30
ewaltari
closed
1 year ago
1
ete3 install needs changing
#29
nikishe
closed
1 year ago
2
How to add more marker genes
#28
mudymudy
opened
1 year ago
10
ValueError: fetch called on bamfile without index
#27
CJJ8848
closed
1 year ago
1
Issue with generating files
#26
huangjz2
closed
1 year ago
4
multiprocessing.pool.RemoteTraceback: KeyError: 'X0022'
#25
yuanf28
closed
1 year ago
3
TypeError: __init__() takes 2 positional arguments but 3 were given
#24
marcejuarez90
opened
1 year ago
3
Error with ngm binary
#23
3miumi
opened
1 year ago
4
Can read2tree be run offline and with custom marker gene list?
#22
masudermann
opened
1 year ago
3
[Question] Marker gene for only one species
#21
llk578496
closed
1 year ago
2
record name cleaning
#20
M-Zeeb
closed
1 year ago
2
Installation issue
#19
dhpalmer
opened
1 year ago
5
(Error) KeyError: 'BETVV'
#18
shelkmike
closed
1 year ago
5
16 not all dependencies listed in environmentyml file
#17
alpae
closed
1 year ago
0
Not all dependencies listed in environment.yml file
#16
alpae
closed
1 year ago
0
adding file with cds sequences of marker_genes in tests
#15
alpae
closed
1 year ago
0
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