Align, trim, and tree example

--- tags: N-exo title: Align, trim, and tree example --- # Align, trim, and tree example ## Env setup ```bash # installing mamba if not there yet (enables faster conda installations) conda install -n base -c conda-forge mamba mamba create -n align-trim-and-tree -c conda-forge -c bioconda -c defaults muscle=5.1 trimal=1.4.1 iqtree=2.2.0_beta conda activate align-trim-and-tree ``` ## Test sequences Making file holding test sequences (copy and paste whole codeblock into command-line): ```bash printf ">UOY43881.1 epoxyqueuosine reductase QueH [Enterobacter roggenkampii] MTTAPFIRPQLTLPNGADKLLLHSCCAPCSGEVMEAIQASGIEYTIFFYNPNIHPQKEYLIRKEENIRFA EKHGVPFVDADYDTDNWFERAKGMEWEPERGVRCTMCFDMRFERTALYAAENGFSVISSSLGISRWKNMQ QINDCGQRAAARYPGMVYWDYNWRKQGGSSRMIEISKREQFYQQEYCGCVYSLRDSNLHRKSQGRPLIRI GKLFYGQDDNEK >WP_112144455.1 epoxyqueuosine reductase QueH [Faecalibacterium hattorii] MISMSKQLNFAQQMDEVLKTLGDARPKLLLHACCGPCSSAVLEQLCAHFEITVLYYNPNTWPAEEYHRRG EELERFVAAAHPLGVTVIEDRYDPQEFYSAVAGLENEPERGSRCTVCYRLRMRRAAQYAAEHGFQWFTTT LSISPHKDAKRINEIGQELEAEFGVKHLPSDFKKHNGYLRSLQLSEEYGLYRQDYCGCEFSARARQAPQT HTGPHRG >WP_245392219.1 epoxyqueuosine reductase QueH [Salinicola halophyticus] MSTADERQALRLPEGHAKLLLHSCCAPCSGEVMEALHASGIDYAIFFYNPNIHPKKEYLLRKEENIRFAE QHGIEFIDADYDTDNWFARAKGMEFEPERGIRCTMCFDMRFERTALYAKENGYTLISSSLGISRWKDMNQ INDCGHRAAAPYEGIEYWDYNWRKKGGSKRMIEISKRERFYQQEYCGCVYSLRDSTSTARRRAAT >WP_200559745.1 epoxyqueuosine reductase QueH [Erwinia sp. S43] MSTVERDKLTLPKGANKLLLHSCCAPCSGEVMEALQVSGIDYTIFFYNPNIHPQKEYLLRKEENIRFAEQHGIPFVDADY DTDNWFARAKGMEWEPERGVRCTMCFDMRFERTALYAYENGFPVISSSLGISRWKNMQQINDCGDRAAAPYEGISYWDYN WRKKGGAARMIEISKRERFYQQEYCGCVYSLRDSNLHRKSQGRPLIKLGVLYYGDEDAEGKS " > test-seqs.faa ``` ## Aligning ```bash muscle -align test-seqs.faa -output test-seqs-aligned.faa ``` ## Trimming ```bash trimal -in test-seqs-aligned.faa -out test-seqs-aligned-trimmed.faa -automated1 ``` ## Treeing ```bash iqtree -T 4 -m MFP -B 1000 -s test-seqs-aligned-trimmed.faa -pre iqtree-out ``` ## Output tree The primary output tree file is "iqtree-out.treefile", which is what we'd give to the iToL site. We can rename that like this: ```bash mv iqtree-out.treefile test-seqs.tre ``` And unless we have some reason to dig into them, we can get rid of all of the intermediate files produced by iqtree like this: ```bash rm iqtree-* ```

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