blastn -query Coccomyxa_peltigerae_ITS.fa -db nt -evalue 1e-100 -out Coccomyxa_ITS.bl -outfmt '6 qseqid qlen sacc slen pident length mismatch gapopen qstart qend qframe sstart send sframe evalue bitscore'

cut -f3 Coccomyxa_ITS.bl |sort|uniq|wc -l

(62)

awk '{if($4>3000) print $0}' Coccomyxa_ITS.bl 
 
(0)
 
awk '{if ($12>$13) print $0}' Coccomyxa_ITS.bl 
 
(0)
 
cut -f3 Coccomyxa_ITS.bl |sort|uniq>Coccomyxa_ITS_acc.txt
 
blastdbcmd -db nt -entry_batch Coccomyxa_ITS_acc.txt |../Scripts/GetRedundant.pl >Coccomyxa_ITS.fa
 
grep ">" Coccomyxa_ITS.fa |wc -l
 
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usearch -cluster_fast Coccomyxa_ITS.fa -id 1 -centroids Coccomyxa_ITS_nr.fa -uc Coccomyxa_ITS_groups.txt
 
perl -pi -e 's/^>\s*gi\|\d+\|\w+\|(\w+)\.\d\|.*/>$1/' Coccomyxa_ITS_nr.fa 

mafft Coccomyxa_ITS_nr.fa >Coccomyxa_ITS_aln.fa

../Scripts/GetExcluded.pl Coccomyxa_ITS_aln.fa |pbcopy

trimal -in Coccomyxa_ITS_aln.fa -phylip -select `pbpaste` >Coccomyxa_ITS.phy

phyml -i Coccomyxa_ITS.phy

../Scripts/GetGB.pl Coccomyxa_ITS.gbk heath.obrien@gmail.com <Coccomyxa_ITS_acc.txt

grep LOCUS Coccomyxa_ITS.gbk |wc -l

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../Scripts/ParseHost.pl Asterochloris_ITS.gbk >Asterochloris_ITS_metadata.txt

../Scripts/GetGroups.py -g Coccomyxa_ITS_groups.txt -m Coccomyxa_ITS_metadata.txt > Coccomyxa_ITS_metadata2.txt

mv Coccomyxa_ITS_metadata2.txt Coccomyxa_ITS_metadata.txt 

[ Expanded representative sequences from Lohtander et al. 2003 in Coccomyxa_ITS_metadata.txt ]

wc -l Coccomyxa_ITS_metadata.txt

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../Scripts/AddSig.pl Coccomyxa_ITS.phy_phyml_tree.txt >Coccomyxa_ITS.nwk

cat Coccomyxa_ITS.nwk | ../Scripts/AddMetadata.pl Coccomyxa_ITS_metadata.txt host > Coccomyxa_ITS_host.nwk