Phylogeny Report系统发育分析报告
Generated by phylogeny-flow 0.1.0-r1 at 2026-05-28T17:32:53Z UTC. This static report follows the analysis path from homologous input sequences through alignment, trimming, tree inference, static visualization, methods and provenance.本报告由 phylogeny-flow 0.1.0-r1 于 2026-05-28T17:32:53Z UTC 生成，按同源序列输入、多序列比对、比对修剪、系统发育树推断、静态可视化、方法记录和溯源信息组织结果。
Executive Summary项目总览
These metrics summarize the computational route and give a first-pass view before biological interpretation. They do not by themselves validate homology, orthology, or species-tree conclusions.这些指标概括本次计算路线，用于在正式生物学解释前快速了解分析状态。它们本身不自动证明同源性、直系同源关系或物种树结论。
Workflow and Biological Questions分析流程与生物学问题
The workflow is organized as a chain of biological evidence transformations rather than a file dump. Each step answers a different question about the same sequence set.报告按生物学证据转换链组织，而不是简单堆叠文件。每一步都围绕同一组序列回答不同问题。
Tree Layout Gallery树形布局图集
The same Newick tree is rendered in two complementary default layouts: a readable rectangular tree and a compact circular overview. The top-level 03_results/tree/plots/tree.* files keep the primary layout selected by --plot-layout; if fan is selected as the primary layout, that extra view is also retained.同一棵 Newick 树默认渲染成两种互补布局：便于阅读的矩形树图，以及适合总览的环形树图。顶层 03_results/tree/plots/tree.* 保留 --plot-layout 指定的主图；如果显式选择 fan 作为主布局，则额外保留扇形图。
How to Read This Report如何阅读本报告
A phylogenetic report should be read as evidence plus assumptions. Start from input identity and alignment quality, then review trimming, model choice, support values, and only then discuss biological interpretation.系统发育报告应被理解为“证据 + 假设”。建议先确认输入序列身份和比对质量，再查看修剪、模型选择、支持率，最后再讨论生物学解释。
A tree is only meaningful if the input sequences are homologous and represent the intended gene, protein, marker, or locus.只有输入序列同源并代表预期基因、蛋白、marker 或位点时，树才有解释意义。
MSA columns define which residues are treated as comparable evidence. Poor alignment can dominate topology.多序列比对的列决定哪些残基被当作可比较证据；差的比对会主导拓扑。
Trimming can remove noisy regions, but aggressive trimming can also remove real biological signal.修剪可以去掉噪声区域，但过强修剪也可能去掉真实生物学信号。
This flow infers a gene/protein tree; species history needs orthology, sampling, and often multi-gene evidence.本流程推断的是基因/蛋白树；物种历史需要直系同源判断、采样设计，通常还需要多基因证据。
Reproducibility makes the analysis auditable, but it does not turn every topology into biological truth. Homolog selection, paralogy, recombination, taxon sampling, alignment uncertainty and model choice remain biological decisions.可复现性让分析可审计，但不会把每一种拓扑自动变成生物学真相。同源序列选择、旁系同源、重组、物种采样、比对不确定性和模型选择仍然是生物学决策。
What Each Step Means每一步意味着什么
Phylogeny starts from a claim that sequences share ancestry. Database hits, marker identity, orthogroups, or curated protein families are common ways to justify that claim.系统发育分析始于“这些序列共享祖先”的判断。数据库命中、marker 身份、orthogroup 或人工整理蛋白家族都可以为这一判断提供依据。
The alignment converts sequences of different histories and lengths into site-wise comparable evidence. Insertions, deletions and divergent regions are where many errors enter.比对把不同长度和演化历史的序列转换成逐位点可比较证据；插入、缺失和高度分化区域往往是误差来源。
IQ-TREE performs model-based maximum-likelihood inference, while FastTree provides a faster approximate route. Speed, model richness and support interpretation differ.IQ-TREE 进行基于模型的最大似然推断，FastTree 提供更快的近似路线。二者在速度、模型丰富度和支持率解释上不同。
Support values describe stability under a method and dataset, not absolute truth. Low support suggests fragile splits; high support still depends on input correctness.支持率描述某种方法和数据集下的稳定性，不是绝对真理。低支持提示分支脆弱；高支持也仍依赖输入是否正确。
Branch lengths usually reflect inferred substitutions per site. They are not calendar time unless a time-calibrated model is explicitly used.分支长度通常表示每个位点的推断替换数；除非显式使用时间校准模型，否则它不是日历时间。
Rectangular and circular layouts are complementary views of the same tree. A prettier layout can help communication, but the canonical result remains the Newick tree.矩形和环形布局是同一棵树的互补视图。更漂亮的布局有助于沟通，但规范结果仍是 Newick 树。
Evidence Tables证据表格
The tables below are the audit layer behind the report. They make the HTML readable by humans while keeping the run inspectable by scripts.下面这些表格是报告背后的审计层。HTML 便于人阅读，TSV 表格则让脚本也能检查结果。
Flow summary流程摘要
| metric | value |
|---|---|
| flow_version | 0.1.0-r1 |
| input_mode | raw_fasta |
| sequence_count | 24 |
| seq_type | protein |
| aligner | mafft |
| trimmer | trimal |
| tree_engine | iqtree |
| final_tree | 03_results/tree/tree.nwk |
| tree_plot_status | generated |
| tree_plot_dir | 03_results/tree/plots |
| tree_plot_layout | rectangular |
| tree_plot_gallery_layouts | rectangular,circular |
| tree_plot_formats | pdf,png,svg |
| tree_plot_style | journal |
| tree_plot_label_align | none |
| tree_plot_label_transform | pretty |
| tree_plot_scale_bar | auto |
| trimmed_alignment | 03_results/alignment/trimmed.fa |
Input summary输入摘要
| metric | value |
|---|---|
| input_mode | raw_fasta |
| sequence_count | 24 |
| seq_type | protein |
| min_length | 104 |
| median_length | 105 |
| max_length | 112 |
Alignment statistics比对统计
| metric | value |
|---|---|
| sequence_count | 24 |
| alignment_length | 116 |
| non_gap_columns | 116 |
| gap_fraction | 0.085848 |
| variable_sites | 71 |
Trimming summary修剪摘要
| metric | value |
|---|---|
| trimmer | trimal |
| mode | automated1 |
| input_alignment_length | 116 |
| trimmed_alignment_length | 104 |
| columns_removed | 12 |
Model summary模型摘要
| metric | value |
|---|---|
| tree_engine | iqtree |
| model | LG |
| model_source | LG |
Support summary支持率摘要
| metric | value |
|---|---|
| tree_engine | iqtree |
| bootstrap_type | UFBoot |
| bootstrap_replicates | 0 |
| alrt_replicates | 0 |
Plot gallery index树图索引
| layout | svg | png | summary | annotations | |
|---|---|---|---|---|---|
| rectangular | 03_results/tree/plots/rectangular/tree.svg | 03_results/tree/plots/rectangular/tree.png | 03_results/tree/plots/rectangular/tree.pdf | 03_results/tree/plots/rectangular/tree_plot_summary.tsv | 03_results/tree/plots/rectangular/tree_tip_annotations.tsv |
| circular | 03_results/tree/plots/circular/tree.svg | 03_results/tree/plots/circular/tree.png | 03_results/tree/plots/circular/tree.pdf | 03_results/tree/plots/circular/tree_plot_summary.tsv | 03_results/tree/plots/circular/tree_tip_annotations.tsv |
Primary plot summary主图摘要
| metric | value |
|---|---|
| tree_file | cytc-out/03_results/tree/tree.nwk |
| tip_count | 24 |
| internal_node_count | 22 |
| metadata_file | NA |
| metadata_id_column | NA |
| metadata_rows | 0 |
| metadata_matched_tips | 0 |
| metadata_unmatched_tips | human_P99999_Homo,chimpanzee_P99998_Pan,rhesus_macaque_P00002_Macaca,horse_P00004_Equus,bovine_P62894_Bos,pig_P62895_Sus,rabbit_P00008_Oryctolagus,mouse_P62897_Mus,rat_P62898_Rattus,chicken_P67881_Gallus,king_penguin_P00017_Aptenodytes,mallard_P00020_Anas,alligator_P81280_Alligator,snapping_turtle_P00022_Chelydra,bullfrog_P00024_Aquarana,zebrafish_Q6IQM2_Danio,common_carp_P00026_Cyprinus,kangaroo_P00014_Macropus,honeybee_P00038_Apis,c_elegans_P19974_Caenorhabditis,budding_yeast_P00044_Saccharomyces,arabidopsis_P29380_Arabidopsis,rice_Q0DI31_Oryza,gorilla_Q6WUX8_Gorilla |
| label_map_file | cytc-out/00_inputs/sequence_id_map.tsv |
| label_map_from | safe_id |
| label_map_to | original_id |
| label_map_rows | 24 |
| layout | rectangular |
| style | journal |
| label_align | none |
| label_transform | pretty |
| scale_bar | auto |
| scale_bar_width | 0.1 |
| scale_bar_label | 0.1 |
| title | phylogeny-flow tree - rectangular |
| formats | pdf,png,svg |
| plot_width | 10.36 |
| plot_height | 7.26 |
| output_files | tree.pdf,tree.png,tree.svg |
Aligned variable sites: 71. Alignment gap fraction: 0.085848.比对中的变异位点：71。gap 比例：0.085848。
Deliverables and Output Structure交付文件与输出结构
The output directory is designed to be copied or archived as a complete result package. The HTML is the entry point, while TSV, FASTA, Newick and log files remain reusable.输出目录可以作为完整结果包复制或归档。HTML 是入口，TSV、FASTA、Newick 和日志文件仍可被复用。
Canonical final Newick tree.规范最终 Newick 树。
Primary plot plus rectangular and circular layout subdirectories; optional fan output appears only when requested as the primary layout.主图以及矩形、环形布局子目录；扇形图只在显式设为主布局时出现。
Aligned and trimmed FASTA plus alignment statistics.比对、修剪后的 FASTA 以及比对统计。
Bilingual HTML report, methods, commands, versions and flow summary.双语 HTML 报告、方法、命令、版本和流程摘要。
Final Newick tree最终 Newick 树
(human_P99999_Homo:0.0000000000,(chimpanzee_P99998_Pan:0.0000010000,(rhesus_macaque_P00002_Macaca:0.0000010000,((((horse_P00004_Equus:0.0322821101,(bovine_P62894_Bos:0.0000010000,pig_P62895_Sus:0.0000010000):0.0000010000):0.0204671439,((rabbit_P00008_Oryctolagus:0.0202661987,(mouse_P62897_Mus:0.0000010000,rat_P62898_Rattus:0.0000010000):0.0000010000):0.0000010000,((((chicken_P67881_Gallus:0.0100558661,king_penguin_P00017_Aptenodytes:0.0100063188):0.0099341418,mallard_P00020_Anas:0.0100988562):0.0133800352,(alligator_P81280_Alligator:0.0299760376,snapping_turtle_P00022_Chelydra:0.0124674457):0.0371726893):0.0213745361,(bullfrog_P00024_Aquarana:0.0516719492,(zebrafish_Q6IQM2_Danio:0.0000010000,common_carp_P00026_Cyprinus:0.0305873732):0.0554760330):0.0215599525):0.0249352129):0.0101557716):0.0000010000,kangaroo_P00014_Macropus:0.0413654074):0.0197299328,((honeybee_P00038_Apis:0.0517514743,c_elegans_P19974_Caenorhabditis:0.4538441075):0.0943831015,((budding_yeast_P00044_Saccharomyces:0.2724551317,arabidopsis_P29380_Arabidopsis:0.2443780200):0.1432699350,rice_Q0DI31_Oryza:0.3161014928):0.0892957878):0.1083095371):0.0552937499):0.0101050190):0.0000010000,gorilla_Q6WUX8_Gorilla:0.0000000000);
Provenance and Reuse溯源与复用
Commands, versions, methods and manifest files are preserved so the run can be reviewed, cited, or reproduced later.命令、版本、方法和 manifest 会被保留，便于后续审计、引用或复现。
Versions版本
| tool | version | source |
|---|---|---|
| phylogeny-flow | 0.1.0-r1 | taffish flow |
| taf-seqkit | 2.13.0-r2 | taffish dependency |
| taf-mafft | 7.525-r3 | taffish dependency |
| taf-trimal | 1.5.1-r1 | taffish dependency |
| taf-iqtree | 3.1.2-r1 | taffish dependency |
| taf-fasttree | 2.2.0-r1 | taffish dependency |
| taf-clipkit | 2.12.0-r1 | taffish dependency |
| taf-muscle | 5.3-r4 | taffish dependency |
| taf-clustal-omega | 1.2.4-r1 | taffish dependency |
| taf-bioconductor-bioviz | 3.23-r2 | taffish dependency |
This report preserves a reproducible command-level tree analysis. It does not search homologs, determine orthology, detect recombination, time-calibrate divergence, or replace expert review of the biological system.本报告保留一条命令级可复现的建树分析。它不负责搜索同源序列、判定直系同源、检测重组、做分歧时间校准，也不替代对具体生物系统的专业审阅。