'trees' 검색 결과

Analyze existing evolutionary trees and other hierarchical trees with ETE 4. Edit branches, add annotations, compare branching structures, explore large trees interactively, and render figures for publication using the appropriate optional visualization components.

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• Prune selected species and change a tree's root
• Compare branching structures between two trees
• Add NCBI or GTDB taxonomy information

Clean up git worktrees across your repos: list every worktree, classify it as merged, remote-only, local-only or dirty, recap what each holds, and remove only the merged clean ones after GO. Use for "clean up worktrees", "what is in my aos-wt folders", "land my worktrees", "prune worktrees".

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Build evolutionary trees from related nucleotide or protein sequences using MAFFT with IQ-TREE or FastTree. Review branch support, a measure of evidence for each grouping, and produce tree summaries and optional visualizations.

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• Build gene trees from related nucleotide sequences
• Compare evolutionary relationships within protein families
• Review branch support and analysis logs

Manage parallel feature development with Git worktrees, separate working folders for different branches. Assign distinct ports, copy environment files, optionally install dependencies, and check for uncommitted changes and merged branches before removing outdated worktrees.

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• Develop several feature branches at the same time
• Prepare a separate workspace for an urgent hotfix
• Give each AI agent its own branch and working folder

Configure GSD through an interactive questionnaire. Choose a model profile and turn workflow features such as research, verification, and code review on or off, then merge the choices into the existing configuration.

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• Change the model profile used by GSD
• Turn research and verification on or off
• Review TDD and code review settings

Create, manage, and cleanup git worktrees with Claude Code agents across all projects. USE THIS SKILL when user says "create worktree", "spin up worktrees", "new worktree for X", "worktree status", "cleanup worktrees", "sync worktrees", or wants parallel development branches. Also use when creating PRs from a worktree branch (to update registry with PR number). Handles worktree creation, dependency installation, validation, agent launching in Ghostty, and global registry management.

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Verify, customize, or opt out of moflo's AUTOMATIC durable-learning sharing across git worktrees / Conductor workspaces on one machine. As of the worktree-auto-sharing change this is on by default — learnings converge across a repo's worktrees with no setup. Use when the user asks "is memory shared across my worktrees?", "where are my worktree learnings stored?", "turn off worktree memory sharing", "share learnings across my separate clones", or "point my worktrees at a custom store". For a team or cross-machine (git-tracked) sharing, use /memory-team instead.

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Coordinate multiple AI agents with assigned owners, clear work boundaries, and a Kanban board that tracks progress. Organize separate branches or worktrees, collect test and handoff evidence, and define checks that must pass before combining their work.

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• Assign parallel tasks to multiple AI agents
• Track progress and blockers across sessions
• Separate editing work across branches or worktrees

Compare changes across Git worktrees, branches, and pull requests through a facilitated discussion between agents. Produce one consolidation plan covering the target worktree, merge order, conflicts, and decisions that need human input.

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• Planning how to combine work from multiple branches
• Comparing overlapping changes and competing implementations
• Reviewing recent worktrees together

Analyze biological sequences and microbial communities in Python. Process and align DNA, RNA, or proteins, build evolutionary trees, calculate diversity, visualize sample differences, test group differences, and convert common biological file formats.

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• Calculate and compare microbiome diversity
• Align DNA, RNA, or protein sequences
• Build and compare evolutionary trees

Set up Herdr Kit and its Mastra Code integration, manage repository synchronization, and create or remove managed worktrees, separate working copies for review or development. The workflow checks supported operations and verifies the resulting manager state.

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• Installing Herdr Kit and the Mastra Code integration
• Keeping repositories synchronized after closing their workspaces
• Creating or removing managed Review and Work worktrees

Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.

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Building modular, debuggable AI behaviors using behavior trees for game NPCs and agentsUse when "behavior tree, bt, npc ai, ai behavior, game ai, decision tree, blackboard, ai, behavior-trees, npc, game-ai, decision-making, agents" mentioned.

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Manage git worktrees across any repository with the `gwm` Rust binary (CLI + ratatui TUI). Use when the user asks to create / list / remove / bootstrap / switch / link worktrees, run a command across worktrees (`gwm exec`) or reclaim build artifacts (`gwm clean`), materialise a PR into a worktree (`gwm review`), drive a multi-repo workspace (`--workspace`), run the JSON daemon / statusline (`gwm daemon`, `gwm statusline`), list or pin AI-agent sessions per worktree (`gwm agents`, Claude Code / Codex / opencode / Mistral Vibe detection), seed config from a preset (`gwm init --preset`), diagnose with `gwm doctor`, drive tmux/zellij, or wire `gcd` via `gwm shell-init`. Also covers multi-forge (#419): GitHub via `gh` **or** GitLab via `glab`, the `forge` / `[forge_hosts]` keys, and `gwm trust add`. Triggers on `gwm`, `gwq`, `git worktree`, `.gwm.toml`, `forge`, `forge_hosts`, `glab`, `gwm trust add`, GitLab MR, `gwm create`, `gwm list`, `gwm exec`, `gwm clean`, `gwm review`, `gwm daemon`, `gwm statusline`, `gwm agents`, `gwm note`, `gwm bootstrap`, `gwm doctor`, `gwm switch`, `gwm tmux`, `gwm zellij`, `gwm link`, `gwm status`, `gwm shell-init`, `gcd`, `feat/#`, `fix/#`, GitHub issue/PR linking on a worktree.

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Report which local git worktrees under tmp/ are safe to close, need a human look, or are explicitly protected. Use when the user says /fleet-audit, asks what worktrees can be cleaned up, or wants a status check across all Ralph-loop/spike worktrees before running closeout on any of them.

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Meta-agent supervisor that manages a fleet of Claude Code agents running in tmux windows. Auto-discovers spare worktrees, spawns agents, monitors state, kicks idle agents, approves safe confirmations, and recycles worktrees when done. TRIGGER when user asks to supervise agents, run parallel tasks, manage worktrees, check agent status, or orchestrate parallel work.

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Initialize a worktree-based repo layout for parallel development. Creates a main worktree, a reviews worktree for PR reviews, and N numbered work branches. Handles .env creation, dependency installation, and branchlet config. TRIGGER when user asks to set up the repo from scratch, initialize worktrees, bootstrap their dev environment, "setup repo", "setup worktrees", "initialize dev environment", "set up branches", or when a freshly cloned repo has no sibling worktrees.

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Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.

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Expert-level data structures covering arrays, linked lists, trees, heaps, hash tables, graphs, and advanced structures like segment trees, tries, and union-find.

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Create isolated git worktrees with smart directory selection and safety verification

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Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DTL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.

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Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DTL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.

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Permanent-delete grooming for leftover Docker builds, agent worktrees, and .next caches. Use when creating or finishing a git worktree, after a local docker build, when the disk is full, or when /tmp or .wt trees were left behind.

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dotfiles の Neovim Treesitter parser runtime を Home Manager と templates のどちらに置くべきか判断し、必要な Nix とドキュメントを更新するためのスキル

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