Difference between revisions of "2017 Mar Taeyoung Lab note"
From Crop Genomics Lab.
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===Jat species cdhited blast na1 again=== | ===Jat species cdhited blast na1 again=== | ||
/alima9002/63_backup/Jatropha/CDS/cdhit_blast_na1$ python blastp.py | /alima9002/63_backup/Jatropha/CDS/cdhit_blast_na1$ python blastp.py | ||
+ | |||
+ | ==2017.3.14== | ||
+ | ===Phylip alignment=== | ||
+ | clustalw -ITERATION=ALIGNMENT -INFILE=%s -ALIGN -TYPE=PROTEIN -OUTPUT=PHYLIP -OUTFILE=%s.phylip | ||
+ | |||
+ | ===Phyml=== | ||
+ | /alima9002/program/PhyML-3.1/PhyML-3.1_linux64 -i %s -d aa -b 500 -m JTT |
Revision as of 05:46, 14 March 2017
Contents |
2017.3.2
Venn diagram using Organ data
Flower and Endosperm data were merged
python ~/py/MakeBinaryTableForOrthomcl.py group.txt > group.txt.binary.flr.and.end python ~/py/change_raw_and_col.py group.txt.binary.flr.and.end > group.txt.binary.flr.and.end.parsed python ~/py/MakeRawInputUsingBinary.py group.txt.binary.flr.and.end.parsed > group.txt.binary.flr.and.end.parsed.rawfile ..
2017.3.6
OrthoMcl again with cdhit file
True Orthologous retrieving
comparing length of peptide sequences with cutoff 0.1
/alima9002/63_backup/Jatropha/CDS/cdhit_blast_na1$ python length_polyporphism.py True_orhthologous.txt > True_orhthologous.txt.length.cutoff.0.1
BEAST analysis
Make Raw File
Alignment
/alima9002/63_backup/Jatropha/CDS/cdhit_blast_na1/Fafile$ python clustalw.py
2017.3.7
BEAST analysis
Make xml file
2017.3.8
Organ transcriptome cdhited OrthoMcl
BLAST
/alima9002/63_backup/Jatropha/OrthoMCL/Organ_cdhit$ blastp -db goodProteins.fasta -query goodProteins.fasta -outfmt 6 -out goodProteins.fasta.allvall -num_threads 8 -evalue 1e-5 -seg yes -soft_masking true -max_target_seqs 999999999
BEAST using no length polyporphism loci
Prottest for select best substitution model
/data2/alima90/Jatropha/same_length_BEAST/$ python prottest.py
retrieve only JTT
/data2/alima90/Jatropha/same_length_BEAST/JTT$ python ret_JTT_only.py
Make xml template using beauti
JTT/length of chain : 50 million
Make xml
/data2/alima90/Jatropha/same_length_BEAST/JTT$ python beast.xml.parsing.py Jct_10060_c0_g1_i1.xml
Running BEAST
/data2/alima90/Jatropha/same_length_BEAST/JTT$ python run_beast.py
KaKs to filter more loci in BEAST analysis
Jat species cdhited blast na1 again
/alima9002/63_backup/Jatropha/CDS/cdhit_blast_na1$ python blastp.py
2017.3.14
Phylip alignment
clustalw -ITERATION=ALIGNMENT -INFILE=%s -ALIGN -TYPE=PROTEIN -OUTPUT=PHYLIP -OUTFILE=%s.phylip
Phyml
/alima9002/program/PhyML-3.1/PhyML-3.1_linux64 -i %s -d aa -b 500 -m JTT