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LTR_retriever
LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/
GNU General Public License v3.0
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low LAI when using ltrharvest result as input
#173
shiyi-pan
opened
1 week ago
0
LTR_retriever produce different result in different data combine ways
#172
LQ16
opened
3 weeks ago
0
Calculated LAI is too large
#171
yaoxkkkkk
opened
1 month ago
3
Kimura2Paramter to ks value/Time
#170
manoharbisht1998
opened
2 months ago
2
LTR retriever is not compatible with RepeatModeler2 since v2.9.8?
#169
BitaoQiu
opened
2 months ago
5
Exploring the transposition profile of specific LTRs
#168
shuren7
opened
2 months ago
2
Assessing Chrysanthemum lavandulifolium genome assembly
#167
zhangdeng1992
opened
3 months ago
2
Dependency checker looking in wrong directory for makeblastdb
#166
benfulton
opened
3 months ago
1
The LTR_retriever fails to identify LTRs with tandem repeats, such as Dasheng.
#165
CSU-KangHu
opened
3 months ago
3
A reviewer's comment related to the setting of mutaion rate
#164
zhdang
closed
2 months ago
2
same bug before about LTR.identifier.pl
#163
Z1997B
opened
4 months ago
3
cleanup.pl Bug?
#162
asgray
opened
4 months ago
3
Are there any changes in Module 1 between versions 2.9.0 and 2.9.9?
#161
ala98412
opened
5 months ago
2
LTR_retriever failed to generate a file - data passing in a multithreaded run
#160
cyycyj
closed
6 months ago
2
fa.mod.nmtf.pass.list is empty
#159
44314474
closed
6 months ago
2
an error in Calculate LAI from EDTA
#158
chaimol
closed
10 months ago
2
LOC list New_genome.nextpolish.exceptChl.FINAL.fa.retriever.scn.full is empty
#157
cutykaka
closed
10 months ago
3
ERROR: No candidate is found in the file(s) you specified.
#156
Janz-Sicau
closed
6 months ago
10
awk: cannot open N02.fa.retriever.scn.extend.fa.rexdb.cls.tsv
#155
renmiaozhen
closed
6 months ago
5
awk: fatal: cannot open file `genome.fa.mod.retriever.scn.extend.fa.rexdb.cls.tsv' for reading (No such file or directory)
#154
OSfish123
closed
10 months ago
1
Invalid value for shared scalar
#153
SamCT
closed
11 months ago
10
I can´t install LTR_retriever via conda
#152
jplondono14
closed
1 year ago
4
conda install errors
#151
xiekunwhy
closed
1 year ago
1
LAI is not applicable on the current genome assembly
#150
yilunhuangyue
closed
1 year ago
3
No tbl file issue
#149
wrengs
closed
1 year ago
5
Running Ltr_retriever...Died at /app/RepeatModeler-2.0.4/LTRPipeline line 693.
#148
ShirelyI
closed
1 year ago
2
ask for help? panLTR
#147
fafuyyk
closed
1 year ago
1
How to discover "sequencing gaps" in genome assemblies.
#146
Wenwen012345
closed
1 year ago
3
A question about LAI in autopolyploid
#145
kedduck
closed
1 year ago
2
RE: Masking LTR
#144
Malabady
closed
1 year ago
2
Total length annotated by RepeatMasker is longer than LTR_retriever
#143
th2ch-g
closed
1 year ago
3
LTR_retriever warning
#142
fafuyyk
closed
1 year ago
1
Are LTRs (insertion time of 0) the likely cause of somatic variation?
#141
Wenwen012345
closed
1 year ago
2
Use of uninitialized value $seq in string eq at call_seq_by_list.pl line 129
#140
wlhCNU
closed
1 year ago
10
No candidate is found in the file(s) you specified
#139
xlmming
closed
1 year ago
2
Can one use EDTA genome.mod.pass.list and genome.mod.EDTA_TEanno.out output in LAI
#138
Chriswinefield
closed
1 year ago
3
Serious error ⇒ Dependency checking: Error: The RMblast engine is not installed in RepeatMasker!
#137
Shokusei
closed
1 year ago
3
Repeatmodeler 、RepeatMasker and LTR_retriever
#136
zuodabin
closed
1 year ago
4
No candidate is found in the file(s) you specified.
#135
cherryDAP
closed
1 year ago
7
No tbl file
#134
aijigekoukou-shen
closed
1 year ago
2
Error: cp: cannot stat *.retriever.scn.adj’: No such file or directory
#133
dmf445
closed
1 year ago
3
too many LTR/unknown and most of LTR/unknown are classified as LTR/Gypsy
#132
shiyi-pan
closed
1 year ago
1
For genus-level TE-annotation
#131
LeeYEAH2
closed
1 year ago
2
LTR insertion time
#130
zuodabin
closed
1 year ago
7
LAI for Big Genome
#129
pxxiao-hz
closed
1 year ago
1
How to run LTR.identifier.pl independently?
#128
xiekunwhy
closed
1 year ago
4
About the proportion of the "unkonwn" item in the genome (".superfam.size.list" file).
#127
Wenwen012345
closed
1 year ago
2
Correct Perl errors and English errors
#126
Ghepardo
closed
2 years ago
1
add $genome permission check
#125
with9
closed
1 year ago
3
add $genome permission check
#124
with9
closed
2 years ago
0
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