28:null 29:["$","title",null,{"children":"Steps to Create a Phylogeny Tree | WabushOnce | Observable"}] 2e:T1b0a,viewof phageTreeInstaller = { const ta = html``; const btn = html``; const script = `# Stop on errors $ErrorActionPreference = "Stop" Write-Host "Installing/checking phage-tree dependencies (Windows PowerShell)..." -ForegroundColor Cyan # ---------------------------- # Settings # ---------------------------- $BlastRoot = "C:\\Tools\\ncbi-blast" $BlastLatestPage = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/" $TempTarGz = Join-Path $env:TEMP "ncbi-blast-latest-x64-win64.tar.gz" # ---------------------------- # 1. Check Python # ---------------------------- Write-Host "" Write-Host "Checking Python installation..." $python = Get-Command python -ErrorAction SilentlyContinue if (-not $python) { Write-Host "Python not found." -ForegroundColor Red Write-Host "Please install Python from https://www.python.org/downloads/" Read-Host "Press Enter to exit" exit 1 } Write-Host "Python found at $($python.Source)" -ForegroundColor Green # ---------------------------- # 2. Install Python packages # ---------------------------- Write-Host "" Write-Host "Upgrading pip and installing Python packages..." python -m pip install --upgrade pip if ($LASTEXITCODE -ne 0) { Write-Host "pip upgrade failed." -ForegroundColor Red Read-Host "Press Enter to exit" exit 1 } python -m pip install --upgrade pandas numpy if ($LASTEXITCODE -ne 0) { Write-Host "Python package installation failed." -ForegroundColor Red Read-Host "Press Enter to exit" exit 1 } # ---------------------------- # 3. Check BLAST+ # ---------------------------- Write-Host "" Write-Host "Checking BLAST+ installation..." $blastn = Get-Command blastn -ErrorAction SilentlyContinue $makeblastdb = Get-Command makeblastdb -ErrorAction SilentlyContinue if ($blastn -and $makeblastdb) { Write-Host "BLAST+ already available on PATH." -ForegroundColor Green Write-Host "blastn: $($blastn.Source)" Write-Host "makeblastdb: $($makeblastdb.Source)" } else { Write-Host "BLAST+ not found on PATH. Installing..." -ForegroundColor Yellow # Confirm tar is available $tarCmd = Get-Command tar -ErrorAction SilentlyContinue if (-not $tarCmd) { Write-Host "The Windows 'tar' command was not found." -ForegroundColor Red Write-Host "Please install BLAST+ manually from:" Write-Host $BlastLatestPage Read-Host "Press Enter to exit" exit 1 } # Make install folder New-Item -ItemType Directory -Force -Path $BlastRoot | Out-Null # Get official directory listing Write-Host "Fetching BLAST+ download page..." $resp = Invoke-WebRequest -UseBasicParsing -Uri $BlastLatestPage # Find latest Windows x64 tar.gz $tarRelative = ($resp.Links | Where-Object { $_.href -match '^ncbi-blast-[^"]+-x64-win64\\.tar\\.gz$' } | Select-Object -First 1 -ExpandProperty href) if (-not $tarRelative) { Write-Host "Could not find a Windows x64 BLAST+ tar.gz package in the official download page." -ForegroundColor Red Write-Host "Open this page and install manually:" Write-Host $BlastLatestPage Read-Host "Press Enter to exit" exit 1 } $tarUrl = $BlastLatestPage + $tarRelative Write-Host "Downloading: $tarUrl" Invoke-WebRequest -UseBasicParsing -Uri $tarUrl -OutFile $TempTarGz if (!(Test-Path $TempTarGz)) { Write-Host "Download failed: $TempTarGz" -ForegroundColor Red Read-Host "Press Enter to exit" exit 1 } # Extract tar.gz Write-Host "Extracting BLAST+..." tar -xzf $TempTarGz -C $BlastRoot # Find bin folder $binDir = Get-ChildItem -Path $BlastRoot -Directory -Recurse | Where-Object { $_.Name -eq "bin" } | Select-Object -First 1 -ExpandProperty FullName if (-not $binDir) { Write-Host "Could not find BLAST bin folder after extraction." -ForegroundColor Red Read-Host "Press Enter to exit" exit 1 } Write-Host "BLAST bin folder: $binDir" -ForegroundColor Green # Add to current session PATH if (($env:PATH -split ';') -notcontains $binDir) { $env:PATH = "$binDir;$env:PATH" Write-Host "Added BLAST bin to current PowerShell session PATH." -ForegroundColor Green } # Add to user PATH for future sessions $userPath = [Environment]::GetEnvironmentVariable("Path", "User") $userParts = @() if ($userPath) { $userParts = $userPath -split ';' | Where-Object { $_ -and $_.Trim() -ne "" } } if ($userParts -notcontains $binDir) { $newUserPath = @($userParts + $binDir) -join ';' [Environment]::SetEnvironmentVariable("Path", $newUserPath, "User") Write-Host "Added BLAST bin to your user PATH for future PowerShell windows." -ForegroundColor Green } else { Write-Host "BLAST bin already present in user PATH." -ForegroundColor Green } # Refresh command lookup $blastn = Get-Command blastn -ErrorAction SilentlyContinue $makeblastdb = Get-Command makeblastdb -ErrorAction SilentlyContinue } # ---------------------------- # 4. Verify Python libraries # ---------------------------- Write-Host "" Write-Host "Verifying Python libraries..." python -c "import pandas, numpy; print('pandas', pandas.__version__); print('numpy', numpy.__version__)" if ($LASTEXITCODE -ne 0) { Write-Host "Python library verification failed." -ForegroundColor Red Read-Host "Press Enter to exit" exit 1 } # ---------------------------- # 5. Verify BLAST commands # ---------------------------- Write-Host "" Write-Host "Verifying BLAST+ commands..." $blastn = Get-Command blastn -ErrorAction SilentlyContinue $makeblastdb = Get-Command makeblastdb -ErrorAction SilentlyContinue if (-not $blastn -or -not $makeblastdb) { Write-Host "BLAST+ install did not complete successfully." -ForegroundColor Red Write-Host "You may need to close and reopen PowerShell." Read-Host "Press Enter to exit" exit 1 } Write-Host "blastn: OK ($($blastn.Source))" -ForegroundColor Green Write-Host "makeblastdb: OK ($($makeblastdb.Source))" -ForegroundColor Green Write-Host "" Write-Host "Dependency installation/check complete." -ForegroundColor Cyan Write-Host "You can now run the phylogeny-tree script." Read-Host "Press Enter to exit" `; ta.value = script; btn.onclick = () => navigator.clipboard.writeText(script); return html`

Install required tools (PowerShell – one-time)

${btn} ${ta}

`; }2f:T19b2,viewof phageTreeInstallerPS = { const { winPath } = phageTreeInputs; if (!winPath || !winPath.trim()) return md`Enter the Windows path above.`; const quotePS = (s) => `"${String(s).replace(/"/g, '""')}"`; const FASTA = winPath.trim(); const lastSlash = FASTA.lastIndexOf("\\"); const WORKDIR = lastSlash >= 0 ? FASTA.slice(0, lastSlash) : "."; const script = `# Stop on errors $ErrorActionPreference = "Stop" Write-Host "Running phage-tree pipeline (PowerShell)..." -ForegroundColor Cyan $FASTA = ${quotePS(FASTA)} $WORKDIR = ${quotePS(WORKDIR)} $OUTDIR = "phage_tree_files" $TREE_NAMED = "phage_tree_named.nwk" Set-Location -LiteralPath $WORKDIR if (!(Test-Path -LiteralPath $FASTA)) { Write-Host "ERROR: FASTA not found: $FASTA" -ForegroundColor Red Read-Host "Press Enter to exit" exit 1 } $blastn = Get-Command blastn -ErrorAction SilentlyContinue $makeblastdb = Get-Command makeblastdb -ErrorAction SilentlyContinue if (-not $blastn -or -not $makeblastdb) { Write-Host "ERROR: BLAST+ is not installed or not on PATH." -ForegroundColor Red Write-Host "Install BLAST+ and confirm these work:" Write-Host " blastn -version" Write-Host " makeblastdb -version" Read-Host "Press Enter to exit" exit 1 } New-Item -ItemType Directory -Force -Path $OUTDIR | Out-Null $OutPath = Join-Path $WORKDIR $OUTDIR Copy-Item -Force -LiteralPath $FASTA -Destination (Join-Path $OutPath "input.fasta") # IMPORTANT: # Move into output folder so BLAST only sees simple relative paths. Set-Location -LiteralPath $OutPath $InputFasta = "input.fasta" $Renamed = "renamed.fasta" $Key = "name_key.tsv" $DB = "phage_db" $Bits = "all_vs_all.bitscore.tsv" $Dist = "dist.phy" $TreeOut = $TREE_NAMED $PyScript = "build_tree.py" Write-Host "Renaming FASTA headers..." $c = 0 if (Test-Path $Key) { Remove-Item -Force $Key } $renamedLines = foreach ($line in Get-Content -Path $InputFasta) { if ($line -match "^>") { $c++ $id = "P{0:D3}" -f $c $orig = $line.Substring(1).Trim() "$id\`t$orig" | Out-File -Append -Encoding utf8 $Key ">$id" } else { $line.Trim() } } $renamedLines | Out-File -FilePath $Renamed -Encoding ascii Write-Host "Building BLAST database..." & makeblastdb -in $Renamed -dbtype nucl -out $DB | Out-Null Write-Host "Running all-vs-all BLAST..." & blastn \` -query $Renamed \` -db $DB \` -outfmt "6 qseqid sseqid bitscore" \` -max_target_seqs 1000 \` -num_threads 8 \` -out $Bits if (!(Test-Path $Bits)) { Write-Host "ERROR: BLAST output file was not created: $Bits" -ForegroundColor Red Read-Host "Press Enter to exit" exit 1 } Write-Host "Writing Python tree-building script..." $py = @' import re import numpy as np import pandas as pd from pathlib import Path BITS = Path("all_vs_all.bitscore.tsv") DIST = Path("dist.phy") KEYF = Path("name_key.tsv") OUTN = Path("phage_tree_named.nwk") if not BITS.exists(): raise FileNotFoundError(f"BLAST output not found: {BITS}") df = pd.read_csv(BITS, sep='\\t', header=None, names=['q','s','bitscore']) if df.empty: raise ValueError("BLAST output is empty. Cannot build tree.") df = df.groupby(['q','s'], as_index=False)['bitscore'].max() mat = df.pivot(index='q', columns='s', values='bitscore').fillna(0.0) names = sorted(set(mat.index) | set(mat.columns)) mat = mat.reindex(index=names, columns=names, fill_value=0.0) diag = np.diag(mat.values).astype(float) diag[diag == 0] = 1.0 norm = mat.values / diag[:, None] dist = 1.0 - norm dist[dist < 0] = 0.0 np.fill_diagonal(dist, 0.0) with open(DIST, 'w', encoding='utf-8') as f: f.write(f"{len(names)}\\n") for n, r in zip(names, dist): f.write(f"{n[:10]:<10} " + " ".join(f"{v:.6f}" for v in r) + "\\n") def nj(names, D): n = len(names) nodes = {i: names[i] for i in range(n)} active = list(range(n)) distmap = {(i, j): D[i][j] for i in range(n) for j in range(n) if i != j} nid = n def d(i, j): return distmap.get((i, j), distmap.get((j, i), 0.0)) def setd(i, j, v): distmap[(i, j)] = v distmap[(j, i)] = v while len(active) > 2: m = len(active) r = {i: sum(d(i, j) for j in active if j != i) for i in active} i, j = min( ((i, j) for i in active for j in active if i < j), key=lambda x: (m - 2) * d(*x) - r[x[0]] - r[x[1]] ) dij = d(i, j) li = 0.5 * dij + (r[i] - r[j]) / (2 * (m - 2)) lj = dij - li li = max(li, 0.0) lj = max(lj, 0.0) u = nid nid += 1 nodes[u] = f"({nodes[i]}:{li:.6f},{nodes[j]}:{lj:.6f})" for k in active: if k not in (i, j): setd(u, k, max(0.5 * (d(i, k) + d(j, k) - dij), 0.0)) active = [x for x in active if x not in (i, j)] + [u] distmap = {k: v for k, v in distmap.items() if i not in k and j not in k} a, b = active return f"({nodes[a]}:{d(a,b)/2:.6f},{nodes[b]}:{d(a,b)/2:.6f});" nwk = nj(names, dist.tolist()) key = {} with open(KEYF, encoding='utf-8') as f: for line in f: line = line.rstrip('\\n') if not line: continue k, v = line.split('\\t', 1) key[k] = v pat = re.compile(r'([\$,])((?:P\\d{3}))([:\$,;])') nwk2 = pat.sub(lambda m: m.group(1) + key.get(m.group(2), m.group(2)) + m.group(3), nwk) with open(OUTN, 'w', encoding='utf-8') as f: f.write(nwk2 + '\\n') print("Wrote", OUTN) '@ $py | Out-File -FilePath $PyScript -Encoding utf8 Write-Host "Computing distance matrix and NJ tree..." python $PyScript if ($LASTEXITCODE -ne 0) { Write-Host "ERROR: Python tree-building step failed." -ForegroundColor Red Read-Host "Press Enter to exit" exit 1 } if (!(Test-Path $TreeOut)) { Write-Host "ERROR: Final tree file was not created: $TreeOut" -ForegroundColor Red Read-Host "Press Enter to exit" exit 1 } Write-Host "DONE." -ForegroundColor Green Write-Host "All files are in:" Write-Host " $OutPath" Write-Host "Final tree file:" Write-Host " $(Join-Path $OutPath $TREE_NAMED)" Read-Host "Press Enter to exit" `; const ta = html``; const btn = html``; ta.value = script; btn.onclick = () => navigator.clipboard.writeText(script); return html`

${btn} ${ta}

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Browse to \n PhageScope's 'Tree Construction Tool'\n\n2. Upload your .fasta file and click Submit\n3. Select the Workspace menu to view result","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":160,"value":"- Take a screen shot of the generated tree and edit in PowerPoint or\n- Change its appearance by downloading the .phy file and editing it in iTol ([**instructions below**](#iTol)).","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":35,"value":"Newark = md`---\n## Create a Phylogeny Tree using a File > 10MB \n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":52,"value":"If utilities are not installed, expand the **\"Install required tools\"** item below and copy and paste the code in Windows PowerShell. (Start Menu | PowerShell)","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":45,"value":"$2e","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":83,"value":"2. Enter the path to your FASTA file below.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":21,"value":"viewof phageTreeInputs = Inputs.form({\n winPath: Inputs.text({\n label: \"📂 Full path to FASTA file (Windows)\",\n placeholder: \"C:\\\\Users\\\\YourName\\\\Desktop\\\\phages\\\\phage_set.fasta\",\n style: \"width: 700px\"\n })\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":28,"value":"$2f","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":60,"value":"iTol = md`--- \n## Redesign a Phylogeny Tree using iTol \n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":65,"value":"1. Create Free iTol account https://itol.embl.de/\n
iTOL is free to use, but saving visualization settings (e.g., font size) requires a ~$5 one-month subscription.\n3. Run the following steps in iTOL (See image below)\n 1. Click \"My Trees\"\n 2. Click \"Tree Upload\"\n 3. Enter a Name for the File\n 4. Click \"Select files to upload\" and select your Tree (.newark) file.\n\n![image@4.png](${await FileAttachment(\"image@4.png\").url()})","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":70,"value":"### Editing the Tree Diagram in iTOL\nI edited the items in the yellow boxes to:\n- Increase the text size and thickness of the branches\n- Try setting \"Branch Lengths\" to Ignore\n- Rotate the tree as desired\n- The names of the phages can be edited by right mouse clicking on the phage name.\n\n![image@1.png](${await FileAttachment(\"image@1.png\").url()})","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":76,"value":"### Saving the file to SVG or PNG\n1. Click the Export Tab\n2. Select a Format (SVG or PNG)\n3. Select an Export Area - I select \"Screen\"\n4. Click Export\n\n![image@5.png](${await FileAttachment(\"image@5.png\").url()})","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"}],"files":"$W30","stdlib":"1","titling":"auto"}} 2d:"$2c:body"