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faircloth-lab
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phyluce
software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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Phasing UCE alleles: phyluce_snp_bwa_multiple_align terminating with errors
#193
christinethacker
closed
3 years ago
5
Error Java not installed when using illumiprocessor
#192
Lostinthecodingsauce
closed
3 years ago
7
phyluce_assembly_get_match_counts
#191
probstrodolfo
closed
4 years ago
1
match_contigs_to_probes_error
#190
fuchs-j
closed
3 years ago
2
ABySS assembly problem on HPC cluster (ABySS version issue?)
#189
PopGen33
closed
4 years ago
2
Internal trimming step problem
#188
Ofsm
closed
3 years ago
6
phyluce_snp_screen_phased_alignments error sequence not the same length?
#187
ymilesz
closed
4 years ago
1
Velvet indexError: list index out of range
#186
Ofsm
closed
4 years ago
0
phyluce_probe_get_multi_merge_table failed to retrieve correctly conserved loci
#185
gushiro
closed
3 years ago
3
trimming, fail?
#184
Ofsm
closed
4 years ago
0
Error while using phyluce_probe_strip_masked_loci_from_set
#183
bheimbu
closed
3 years ago
2
phyluce_probe_strip_masked_loci_from_set error
#182
fanvanf
closed
3 years ago
3
phyluce_assembly_assemblo_trinity failed due to the file exists
#181
liugang9988
closed
3 years ago
3
issue with abyss assembly: AttributeError: 'Seq' object has no attribute 'tostring'
#180
kkmills
closed
3 years ago
5
phyluce_assembly_get_trinity_coverage gatk issue
#179
mprebus
closed
4 years ago
2
trinity/abyss assembly error: "The appear to be multiple files for R1/R2/Singleton reads"
#178
kkmills
closed
3 years ago
11
phyluce_snp_convert_vcf_to_structure
#177
quattrinia
closed
3 years ago
2
phyluce_align_format_nexus_files_for_raxml produces empty phylip file
#176
Jesseholmes
closed
4 years ago
4
Trouble with phyluce_align_get_informative_sites
#175
TomSemple
closed
4 years ago
2
phyluce_assembly_get_match_counts
#174
lixiaoyi-12
closed
3 years ago
1
Allow extra specifiers in UCE names (e.g., to imply a probeset namespace)
#173
wmaddisn
opened
4 years ago
0
joined_allele_sequences_all_samples.fasta empty?
#172
ymilesz
closed
3 years ago
11
phyluce_assembly_match_contigs_to_probes gives error AttributeError: 'NoneType' object has no attribute 'groups'
#171
claudiavaga
closed
4 years ago
2
Handle mafft args
#170
moskalenko
closed
3 years ago
0
Trinity not working: IOError: Neither Trinity.fasta nor trinity.log were found in output.
#169
claudiavaga
closed
4 years ago
13
phyluce_probe_slice_sequence_from_genomes error
#168
karlyhiggins
closed
3 years ago
1
Some sequences fail to assemble using phyluce_assembly_assemblo_spades?
#167
ymilesz
closed
4 years ago
3
Edge trimming not depositing UCEs into folder
#166
BenjaminBlanchard
closed
3 years ago
17
Error running "align_get_align_summary_data"
#165
BenjaminBlanchard
closed
4 years ago
3
Calling indels (GATK)
#164
gustavo-miranda
closed
3 years ago
2
Issue running Quality control step in Tutorial 1
#163
BenjaminBlanchard
closed
4 years ago
8
Updating phyluce through conda to 1.6
#162
hintzam33
closed
5 years ago
3
error when running phyluce_assembly_match_contigs_to_probes
#161
fanvanf
closed
3 years ago
4
Fix typo in documentation
#160
caioraposo
closed
5 years ago
0
phyluce_assembly_assemblo_trinity failed: gzip: stdout: Broken pipe
#159
caioraposo
closed
3 years ago
4
ConfigParser.NoSectionError: No section: 'names'
#158
liugang9988
closed
3 years ago
23
Trimming alignment drops all loci
#157
heather340
closed
5 years ago
10
phyluce_align_seqcap_align returns error
#156
mchj74
closed
3 years ago
1
phyluce_assembly_get_match_counts returns NoneType error
#155
mchj74
closed
5 years ago
2
Use phyluce_assembly_get_trinity_coverage for abyss data?
#154
ymilesz
closed
3 years ago
10
phyluce_align_seqcap_align
#153
ClayAssis
closed
5 years ago
10
lastz fails
#152
mchj74
closed
5 years ago
5
Align baits against exemplar genomes
#151
mmaggia
closed
3 years ago
0
phyluce_snp_bwa_multiple_align issue
#150
mprebus
closed
5 years ago
2
phyluce_align_get_only_loci_with_min_taxa not giving the correct number of taxa in output
#149
camilocalderon
closed
3 years ago
8
phyluce_assembly_get_trinity_coverage_for_uce_loci raise IOError("Picard metrics file for {} has more than two lines".format(sample))
#148
KNx5
closed
3 years ago
12
Update tutorial-three.rst
#147
milag6
closed
5 years ago
1
phyluce_snp_bwa_multiple_align fails to merge BAMs - File "/anaconda2/envs/phyluce/bin/phyluce_snp_bwa_multiple_align", line 193, in <module> main() File "/anaconda2/envs/phyluce/bin/phyluce_snp_bwa_multiple_align", line 182, in main bam = picard.merge_two_bams(log, sample, sample_dir, bam, bam_se) File "/anaconda2/envs/phyluce/lib/python2.7/site-packages/phyluce/picard.py", line 124, in merge_two_bams os.remove(bam) OSError: [Errno 2] No such file or directory:
#146
andreluizherpeto
closed
3 years ago
4
phyluce_assembly_get_fastas_from_match_counts error - sequences longer than expected
#145
wjaratlerdsiri
closed
5 years ago
1
phyluce_align_get_smilogram_from_alignments
#144
mcfaddenlab
closed
5 years ago
1
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