cat ~/Downloads/sequences.fasta >> ../Nostoc_rbcX.fa

cat ~/Downloads/sequences.fasta | perl -p -e 's/>gi\|\d+\|\w+\|(\w+)\.\d\|.*/>$1/' > new_seqs.fa

cp ../Nostoc_rbcX_metadata.txt ./

grep ">" new_seqs.fa | perl -p -e 's/>(\w+)/$1\tUNIQUE\tIN TREE\tGunnera magellanica/' >> Nostoc_rbcX_metadata.txt

mafft --add new_seqs.fa ../Nostoc_rbcX_nr_aln.fa >Nostoc_rbcX_aln.fa
 
../Scripts/GetExcluded.pl Nostoc_rbcX_aln.fa |pbcopy

trimal -in Nostoc_rbcX_aln.fa -phylip -select `pbpaste` >Nostoc_rbcX.phy 

phyml -i Nostoc_rbcX.phy 

../Scripts/AddMetadata.pl Nostoc_rbcX_metadata.txt host <Nostoc_rbcX.phy_phyml_tree.txt >Nostoc_rbcX.nwk

../Scripts/ColourTree.pl Nostoc_rbcX.nwk host >Nostoc_rbcX_host.nwk